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An estimated 10-18 percent of the approximately 16 million natives of Saudi Arabia are Shia Muslims, (almost all of the remaining 85-90 percent being Sunni). The modern Kingdom of Saudi Arabia—formed in 1932—was formed as an alliance between the House of Saud and followers of strict Sunni Islamic scholar Muhammad ibn Abd al-Wahhab—often referred to as the "Wahhabi movement" or "Wahhabi mission". Followers of the Wahhabi mission—who dominate religious institutions, courts and education of the kingdom —believe Muslims should return to the interpretation of Islam found in the classical texts, the Quran and the Sunnah. They also believe that self-proclaimed Muslims who seek intercession from holy men—such as the Imams Shia revere and pray to—are not true Muslims.  While attempts to force conversion of Shia have been infrequent, Shia have alleged severe discrimination in Saudi Arabia. Saudi authorities, on the other hand, have suspected that the Islamic Republic of Iran—a Shia power close to Saudi oil fields—has encouraged Saudi Shia to rise up and work for the overthrow of the royal family.
Most Shi'i Muslims belong to the Twelver sect and live in the oil-rich areas of the Eastern Province, with the largest concentrations in oasis of Qatif and Al-Hasa. There is also a Twelver minority in Medina called the Nakhawila, and some Shia have even migrated to the large urban area of Riyadh. Smaller Zaydi and Isma'ili communities also live in Najran along the border with Yemen.
While Saudi Arabia has only been a country since 1932, an earlier Al Saud state (Emirate of Diriyah) clashed with the Shia. Ibn Abdul-Wahhab believed that Shia "imported into Islam" the practice of building mosques on graves, a practice he considered un-Islamic. He referred to Shia as Rafida (rejecters), a name his followers have continued to use.
In 1802, the Saud-Wahhabi alliance waged jihad (or at least qital, i.e. war) on the Shia holy city of Karbala. There, according to a Wahhabi chronicler `Uthman b. `Abdullah b. Bishr:
Muslims [Wahhabis referred to themselves as Muslims, not believing Shia to be Muslims] scaled the walls, entered the city ... and killed the majority of its people in the markets and in their homes. [They] destroyed the dome placed over the grave of al-Husayn [and took] whatever they found inside the dome and its surroundings ... the grille surrounding the tomb which was encrusted with emeralds, rubies, and other jewels ... different types of property, weapons, clothing, carpets, gold, silver, precious copies of the Qur'an."
The main Shia area of what is now Saudi Arabia -- al-Hasa -- was conquered by Saudi forces in 1913. The initial treatment of Shia was harsh, with Shia religious leaders compelled to vow to "cease observance of their religious holidays, to shut down their special places of worship and to stop pilgrimages to holy sites in Iraq." Wahhabi ulama also "ordered the demolition of several Shiite mosques" and took "over teaching and preaching duties at the remaining mosques in order to convert the population."  However within a year, Al-Saud emir Ibn Saud permitted the Shia to expel the Wahhabi preachers and to hold private Shiite religious ceremonies led by the Shiite religious establishment "without interference."
Saudi authorities have however acted on Wahhabi desires to eliminate "vestiges of Shiite religiosity" in and around Medina. In 1926, the Al-Baqi' mausoleum—which included the tombs of the second, forth, fifth, and six Shia Imams—was destroyed by Ibn Saud. In 1975, the tomb of a Shia imam (Ismail ibn Ja'far al-Sadiq) was reportedly destroyed, and a year later an ancient palm tree that legend had it had been planted under the direction of the Prophet Muhammad, and visited by Shiite pilgrims for generations, was cut down on orders of a high ranking Wahhabi shiekh.
In 1979, the Iranian Islamic Revolution overthrew the Shah of Iran, replacing a pro-Western monarchy with an anti-Western revolutionary Islamic republic. Iran is larger than Saudi Arabia and relatively close to Saudi Arabia's oil fields—which is also where most Saudi Shia traditionally lived. It was eager to export its revolution, and ideologically opposed to both monarchies and Muslim countries allied with the West. Leaflets, radio broadcasts and tape cassettes from Iran targeted Saudi Shia and attacked Al Saud for corruption and hypocrisy. That November, Shia celebrated Ashura (illegally) for the first time in many years. In February demonstrations were held on the one year anniversary of Ayatollah Khomeini's return to Iran. Saud officials responded with both "sticks and carrots", arresting activists but also promising more schools, hospitals and infrastructure for the Shia region.
In 1987 Saudi officials were again alarmed after Khomeini "denounced the House of Saud as murderers and called on all loyal Shia in the Kingdom to rise up and overthrow them", following the deaths of over 300 during a demonstration by Iranian pilgrims at hajj.  After oil pipelines were bombed in 1988, the Saudi government accused Shia of sabotage executed several. In collective punishment restrictions were placed on their freedoms and Shia were further marginalized economically. Wahabi ulama were given the green light to sanction violence against Shia. Fatwas were passed by the country’s leading cleric, Abdul-Aziz ibn Baz denouncing Shia as apostates from Islam.
In 2003, the political direction turned again, and a series of "National Dialogues" were initiated that included Shiites (as well as Sufis, liberal reformers, and professional women), to the strong disapproval of Wahhabi purists.
As of 2006, more militant Saudi Wahhabi clerics were circulating a petition calling for an intensification of sectarian violence against the Shiites, while the official religious establishment was calling for Shiites renounce their “fallacious” beliefs voluntarily and embrace “the right path” of Islam, rather than be killed, expelled, or converted by violence.
In modern day Saudi Arabia, the Sunni rulers limit Shia political participation to "notables", according to scholar Vali Nasr. These notables benefit from their ties to power, and in return are expected to control their community. Much political activity takes place outside these parameters. Since 1979, hundreds of Saudi Shiites have been jailed, executed, and exiled.
According to Ondrej Beranek of Brandeis University, Shiite opposition in Saudi Arabia has "undergone various stages of developmental." Saudi Shiites found Ayatollah Khomeini and the Iranian Revolution a "political inspiration", but a "important ideological source" was the organization Harakat al-risaliyin al-tala‘i‘ (literally “the Movement of Vanguards’ Missionaries”), established in 1968 not in Iran but in the Iraqi city of Karbala under the auspices of marja‘ al- taqlid (religious authority) Sayyid Muhammad Mahdi al- Shirazi. Other organizations include Munazzamat al-thawra ‘l-islamiyya (Organization of Islamic Revolution) -- established after the Intifada of 1979. Focusing on peaceful change it changed its name to al-Haraka ‘l-islahiyya (Reform Movement).
In response to this change, King Fahd, met several of al-Saffar's followers and in October 1993 a pact was signed. Fahd promised to work towards improving conditions for Shiites in Saudi Arabia -- ordering the elimination of derogatory terms for Shiites from textbooks, removing certain other forms of explicit discrimination, allowing many Saudi Shiite exiles to return to Saudi Arabia, and other acts. In return, al-Haraka ‘l-islahiyya was dissolved and its members formally agreed to dissociate themselves from foreign groups and movements.
As of 2009, the main spokesman and representative of the Saudi Shiite movement in its more moderate incarnation has been Sheikh Hassan al-Saffar (b. 1958). Al-Saffar represents one of the few voices publicly calling for moderate, pragmatic action, tolerance and reconciliation between Shiites and Sunnis, and a political system based on civil society, free elections and freedom of speech.
At the other end of the Shia political spectrum is the Saudi Hizballah or Hezbollah Al-Hejaz. Established in 1987, it supports the overthrow of the royal government. In 1988 and 1989, Saudi Hizballah led a couple of attacks on oil infrastructure and also murdered Saudi diplomats in Ankara, Bangkok, and Karachi. In 1996 bombed bombing in the Saudi city of al-Khubar. Some of its members went through training in Iran. THe group also is thought to use Iranian training camps in the Biqa‘ valley in Lebanon.
In addition to these two fractions, there are also smaller groups of traditionalists who look at the Saudi regime with suspicion and do not intend to become part of any reconciliation talks.
(The American embassy in Saudi Arabia (as revealed by wikileaks), refers to these two political groupings of Shia in the Eastern Province as Islahiyyah (the Shirazis) and Hezbollah Al-Hejaz (Saudi Hezbollah))
Following the 9/11 attacks and 2003 Riyadh compound bombings, Saudi Arabia seemed determined to stop the brutal campaign against its Shia community, which in previous decades had resulted in hundreds of Shiites being jailed, executed, and exiled. Such a liberal move, however, could easily be understood as merely part of a new campaign aimed at improving the image of Saudi Arabia in the West.
In 1988 fatwas passed by the country’s leading cleric, Abdul-Aziz ibn Baz denounced the Shias as apostates. Another by Abdul-Rahman al-Jibrin, a member of the Higher Council of Ulama is on record as saying
"Some people say that the rejectionists (Rafidha, i.e. Shia) are Muslims because they believe in God and his prophet, pray and fast. But I say they are heretics. They are the most vicious enemy of Muslims, who should be wary of their plots. They should be boycotted and expelled so that Muslims spared their evil."
According to Vali Nasr, al-Jibrin's sanctioning of the killing of Shia was reiterated in Wahhabi religious literature as late as 2002.
Saudi Arabia has no Shia cabinet ministers, mayors or police chiefs, according to another source, Vali Nasr, unlike other countries with sizable Shia populations (such as Iraq and Lebanon) . Shia are kept out of "critical jobs" in the armed forces and the security services, and not one of the three hundred Shia girls’ schools in the Eastern Province has a Shia principal.
Pakistani columnist Mohammad Taqi has written that "the Saudi regime is also acutely aware that, in the final analysis, the Shiite grievances ... stem from socioeconomic deprivation, as a result of religious repression and political marginalization bordering on apartheid."
"Saudi Arabia is a glaring example of religious apartheid. The religious institutions from government clerics to judges, to religious curriculums, and all religious instructions in media are restricted to the Wahhabi understanding of Islam, adhered to by less than 40% of the population. The Saudi government communized Islam, through its monopoly of both religious thoughts and practice. Wahhabi Islam is imposed and enforced on all Saudis regardless of their religious orientations. The Wahhabi sect does not tolerate other religious or ideological beliefs, Muslim or not. Religious symbols by Muslims, Christians, Jewish and other believers are all banned. The Saudi embassy in Washington is a living example of religious apartheid. In its 50 years, there has not been a single non-Sunni Muslim diplomat in the embassy. The branch of Imam Mohamed Bin Saud University in Fairfax, Virginia instructs its students that Shia Islam is a Jewish conspiracy."
The Saudi government has refused to allow Shia teachers and students exemption from school to partake in activities for the Day of Ashura, one of the most important religious days for Shia Muslims which commemorates the martyrdom of Muhammad's grandson, Husayn bin Ali). In 2009, during Ashura commencements, Shia religious and community leaders were arrested protesting against govt and chanting slogans against Wahhabis
Shiites are often banned from building mosques and other religious centers, and sometimes perform Friday prayers in various homes (Al-Hassan). In the Eastern city of Al-Khobar, whose population is predominately Shia, mosques and prayer centers were closed for sometime due to the political activities, beginning in July 2008 but they are now opened. Presently there are 81 Shia mosques in Al Khobar. Saudi Arabia's religious police mandate prayers and all those in public buildings during prayer time are required to stop what they are doing to pray. Because there are minor differences between the way that Shiites and Sunnis pray and between prayer times, Shiites are forced to either pray the Sunni way or take a break from work.
In 2009 a group of Shiites on their way to perform hajj pilgrimage (one of the five pillars of Islam that all able-bodied Muslims are required to perform once in their lives) in Mecca were arrested by Saudi religious police due to the involvement in a protest against Saudi govt.. A fifteen-year-old pilgrim was shot in the chest and an unknown assailant stabbed a Shiite sheikh who played the major role in sparking up the clash between pilgrim and security forces in the back, shouting “Kill the rejectionist [Shia]”.
Religious police have arrested Shia Women in the Eastern Province for matters as trivial as organizing classes for Quranic studies and selling clothing for religious ceremonies as they were involved in political activities which are not allowed in KSA.
In the eastern city of Dammam where three quarters of the 400,000 residents are Shia, there are over 81 large mosques and few hundreds Mussallas, limited Shia call to prayer broadcast, couple of cemeteries for Shia.
Much of education in Saudi Arabia is based on Wahhabi religious material. From a very young age, students are taught that Shiites are not Muslims and that Shiism is a conspiracy hatched by the Jews, and so Shiites are worthy of death. Government Wahhabi scholars, such as Abdulqader Shaibat al-Hamd, have proclaimed on state radio that Sunni Muslims must not “eat their [Shia] food, marry from them, or bury their dead in Muslims' graveyards”.
The government has restricted the names that Shias can use for their children in an attempt to discourage them from showing their identity. Saudi textbooks are hostile to Shiism, often characterizing the faith as a form of heresy worse than Christianity and Judaism.
Because anti-Shia attitudes are engrained from an early age, they are passed down from generation to generation. This prejudice is found not only in textbooks (often characterizing the faith as a form of heresy worse than Christianity and Judaism), but also within the teachers in the classroom, and even in the university setting. (Wahhabi) teachers frequently tell classrooms full of young Shia schoolchildren that they are heretics. Teachers who proclaim that Shiites are atheists and deserve death have faced no repercussions for their actions, barely even receiving punishment. At a seminar about the internet, held in King Abdulaziz City of Science and Technology, professor Dr. Bader Hmood Albader explained how the internet was beneficial to society, but at the same time there were many Shia websites proclaiming to be Muslim websites, which needed to be stopped.
Much discrimination occurs in the Saudi workforce as well. Shiites are prohibited from becoming teachers of religious subjects, which constitute about half of the courses in secondary education. Shiites cannot become principles of schools. Some Shiites have become university professors but often face harassment from students and faculty alike. Shiites are disqualified as witnesses in court, as Saudi Sunni sources cite the Shi'a practise of 'taqiyyah'- wherein it is permissible to lie in any circumstance against non-Shi'as. Shia cannot serve as judges in ordinary court, and are banned from gaining admission to military academies, and from high-ranking government or security posts, including becoming pilots in Saudi Airlines.
Amir Taheri quotes a Shi'ite businessman from Dhahran as saying "It is not normal that there are no Shi'ite army officers, ministers, governors, mayors and ambassadors in this kingdom. This form of religious apartheid is as intolerable as was apartheid based on race." 
Human Rights Watch reports that Shiites want to be treated as equals and desire to be free from discrimination (Human Rights Watch). King Abdullah has attempted to bring Sunnis and Shiites together and advance towards religious tolerance. However, the country as whole has not moved forward and the Shia minority is still marginalized on a large scale.
Shiite pilgrims go to Jannat al Baqi mainly to visit the grave of Fatima and Ahl al-Bayt who are buried in the cemetery of Jannat al-Baqi' but no visit of other great Sahabas in Islam. Many incidences of not following the rules of the place happened by Shiites in this region specifically resulting in the arrest which most of the times were released later. Shias and Sunni Hanafi Wahhabi Sha'afis Barelvis, and Dawoodi Bohra Ismailis usually pray near graves of Ahl al-Bayt but in Wahhabism this act is considered as Shirk. In Saudi Arabia, most of the people follow Quran and Sunnah which is called Wahhabism, So they do not allow anything which has not allowed by Quran and Sunnah like to pray near graves of Ahl al-Bayt in Jannat al Baqi.
Early 2009, several Shiites attacked into the grave of Fatima (who is daughter of Muhammad and the wife of Ali) and grabbed stones, sand and in order to make turbahs out of them which is totally not permissible according to Quran and Sunnah.
Late 2011, a Shiite citizen was charged for not following the law and involved with blasphemy and sentenced to 500 lashes and 2 years in jail; the latter sentence was later reduced. Also late 2011, a prominent Shiite Canadian cleric, Usama al-Attar, was arrested as he insulted the great Sahabi and Khalifa Uthman ibn Affan ra and for criticizing the kingdom's handling of uprisings in Yemen and Bahrain.. He was released on the same day, declaring the arrest entirely unprovoked.
The much smaller Ismāʿīlī minority—also known as Seveners -- differ from the Twelver Shia in their acceptance of Isma'il ibn Jafar as the appointed spiritual successor (Imām), rather than Moosa Al Kazim. There are an estimated 100,000 of them living in the southern region of Najran next to Yemen. They also have been subject to what Human Rights Watch calls "official discrimination," encompassing "government employment, religious practices, and the justice system".
Following the clashes in April 2000, Saudi authorities imprisoned, tortured, and summarily sentenced hundreds of Ismailis, and transferred hundreds of Ismaili government employees outside the region. Underlying discriminatory practices have continued unabated.
In 1997 the director of the Ministry of Islamic Affairs opened an office in Najran for the purpose of propagating Wahhabi doctrine to the local Isma'ilis. Saudi official Sheik Ali Khursan declared Ismaelis to be infidels because they did not follow the Sunna and do not believe that the Qur'an is complete, stating `We don't eat their food, we don't intermarry with them, we should not pray for their dead or allow them to be buried in our cemeteries.` In 1997 the Governor Prince Mish'al ordered police to prevent Ismaelis from performing prayers during the post-Ramadan Islamic festival of Eid al-Fitr. "Anti-Ismaeli campaigns resulted in many arrests and flogging." In April 2000, responding to an Amnesty International campaign publicizing lack of religious freedom in Saudi Arabia, Ismaelis in Najran openly celebrated Ashura for the first time in many years. Shortly thereafter Saudi religious police "stormed a major Ismaeli mosque, seized many of its religious texts and arrested three clerics". Local Ismaelis, who are often armed, retaliated, firing on security forces and burning some of their vehicles. Approximately 40 people were killed and many more injured. Saudi Army reinforcements swept the area and made many arrests. 
Hundreds of Ismaeli government employees were transferred away from Najran. Sometime after August 2000, four Ismaeli high school student were "sentenced to two to four years in prison and 500 to 800 lashes for fighting with a Wahhabi teacher, who openly insulted their religious beliefs in front of other students in the classroom."