In his lifetime, al-Baqir was regarded as a prominent transmitter of prophetic traditions. As a Shia imam, al-Baqir's own sayings and deeds have also been recorded in Shia sources, including some fifteen percent of the traditions collected in the celebrated Man La Yahduruhu al-Faqih|. Such is the extent of his contributions that Shia traditions attributed to al-Baqir and his successor al-Sadiq outnumber all other Shia imams and the prophet combined. As the first Shia imam who engaged in systematic teaching, al-Baqir is also credited with laying the doctrinal and legal foundations of Twelver Shi'ism, which were further developed by al-Sadiq. Contributions of al-Baqir to Twelver doctrine and law are collected in the six-volume , compiled by A. al-Utaridi. Al-Baqir may also be regarded as the father of Isma'ili and Zaydi jurisprudence. Finally, al-Baqir significantly contributed to Twelver exegesis of the Quran and two commentaries are attributed to him.
Contributions to theology Imamate Al-Baqir's doctrine of imamate, further elaborated by his successor al-Sadiq, characterised the necessary qualities of imams, particularly their divinely-inspired designation (Nass (Islam)|), their esoteric knowledge (), and their infallibility (Ismah|), all of which distinguished imams as the best of mankind, representatives of God on earth, and the only source of spiritual guidance. In particular, after Muhammad, they are the only authoritative interpreters of the Quran, the exalted part of which actually refers to them and Muhammad. In contrast, as the executer of religious laws, imamate or caliphate is essentially a political function in Sunni Islam, where caliphs are ideally appointed by consensus, although hereditary caliphate is the norm. In al-Baqir's view, imamate is confined to descendants of the Islamic prophet Muhammad, from the marriage of his daughter Fatima to his cousin Ali ibn Abi Talib. Following a divine mandate, each imam is designated by his predecessor (), beginning with Ali himself who was designated by the prophet at the
Ghadir Khumm. For instance, al-Baqir cited the Quranic verse 2:124, according to which, God designated
Abraham as imam and also granted this favor to those of his progeny who are not evildoers. Crucially, the hereditary nature of imamate in al-Baqir's doctrine closed the field to outside claimants. is often accompanied in Shia sources by inheritance of secret religious scrolls and the prophet's weapons. The latter paralleled the
Ark of the Covenant for the
Israelites. In al-Baqir's doctrine, imams are distinguished by their esoteric knowledge, which they inherited from Ali. In turn, Ali received this knowledge from the prophet, a reference to the well-known prophetic tradition, "I am the city of knowledge and Ali is its gate." In particular, imams know the true exegesis () of the Quran, a reference to the famous
hadith of the, attributed to the prophet. Al-Baqir's doctrine of imamate was thus primarily based on knowledge rather than political power, although he also considered imams entitled to the latter. The divinely-inspired knowledge of imams and prophets are similar but imams could only hear (and not see) the archangels, according to al-Baqir. According to al-Baqir, imams also inherit certain spiritual and primordial lights () referenced in the Quran.Their divine knowledge and spiritual light protect imams from sins, for which al-Baqir cited the
verse of purification. Already in his lifetime, some followers of al-Baqir regarded him as infallible. By implication, al-Baqir's doctrine gave imams absolute spiritual authority over Muslims, resting on the absolute authority of the prophet. His doctrine also held imams as the sole spiritual guides in life and the source of intercession in the afterlife. In al-Baqir's view, imams are the highest proofs ( ) of God and guides towards Him, without whom the world cannot exist for a moment. Not only obedience to imams is obligatory in al-Baqir's interpretation of the
verse of obedience, but love for them is also mandated in his exegesis of the
verse of. Shias thus form an all-encompassing bond of spiritual loyalty (walaya|) with their imams, who are both masters and supportive friends in the journey of the spirit. Identifying his imam is a religious duty for every Muslim, and those who die without knowing their imam have died a death of ignorance (
Jahilliya). Furthermore, willfull opposition to imams is a grave sin and staunch enemies of imams are destined for hellfire. To support his theory, al-Baqir relied on his interpretations of various Quranic verses and prophetic traditions. For instance, al-Baqir emphasised his interpretation of the
verse of, according to which Ali was granted the guardianship () of Muslims, on par with the prophet. According to al-Baqir, fearing backlash from some, the prophet was reluctant to publicly announce the of Ali until he was spurred to do so (at the Ghadir Khumm) by the
verse of tabligh. The prophetic traditions that al-Baqir invoked include the hadith of the Ghadir Khumm and the
hadith of the position.
Nature of God A hotly debated issue at the time was whether the Quran, thought to be the word of God, was created or eternal. Those who believed in predetermination argued that the Quran was eternal for God has always known the events referenced in the Quran. In contrast, those who advocated for free will thought that the Quran was created in time. Al-Baqir held that the Quran was neither created nor eternal. Rather, it is the word of the Creator. More generally, al-Baqir held that all attributes of God were eternal but only as adjectives. For instance, "knowing", "hearing", and "seeing" are how God characterises himself. These help believers understand something about God but are not to be confused with Him. In al-Baqir's view, God is beyond human imagination. He thus advised his followers to discuss God's creation rather than his nature. When asked if he has seen God, al-Baqir responded that God could not be seen by eyes but can be apprehended by the inner reality of faith. On another controversial topic, al-Baqir held that God was a thing, but a thing incomparable to all other things, something neither cognisable nor delimited.
Faith () By definition, a () and a Muslim are characterised, respectively, by the two notions of () and (). Citing the Quranic verse 49:14, al-Baqir defined Muslims as those who
confess Islam in words and outwardly practice Islamic rites, such as praying and fasting. In his view, however, is more exclusive than , that is, the former implies the latter but not vice versa. More specifically, al-Baqir held that is a Muslim with inner faith, a faith demonstrated through fulfillment of religious duties. The foremost among these duties is the to (Shia) imams. There are indeed numerous traditions attributed to al-Baqir about , the importance of which, in his view, is such that one's good deeds would not be accepted without . Yet al-Baqir also curtailed this absolutist perspective by emphasising that cannot be attained without virtue and piety. In addition to , al-Baqir listed the remaining duties of a as (), prayer, fasting, pilgrimage (
Hajj), and (striving in God's way). He also listed (), (), (), and () as the pillars of . Al-Baqir thus identified an intermediate state between and (disbelief). This gray area was further characterised by his successor al-Sadiq, who held that a Muslim who does not harbor enmity towards the
Ahl al-Bayt and their followers is neither nor (disbeliever). That is, such non-Shias are considered Muslims, with their due legal rights, but not (true) believers. By implication, al-Baqir considered righteous action as an integral component of , a view that sharply differed from
Murji'ites and
Kharijites, two contemporary currents. The former did not consider good conduct essential to , with the political implication that dissent and disobedience were discouraged, even if Muslim rulers were corrupt. For Kharijites, in contrast, anyone who committed a mortal sin automatically apostated. In al-Baqir's view, had degrees of perfection and could vary over time. In particular, he held that new (religious) knowledge, when put into action, would strengthen one's . Later Sunni thought similarly adopted the notion of gradated .
Predestination Under Umayyads, predestination, the belief that God has pre-ordained everything, was likely promoted to justify their rule and encourage moral complacency. In contrast, there were others who believed in free will. Among this latter group, some held that all that is good is created by God and everything bad is from men. Al-Baqir rejected both views, saying that there was a third position between predestination and free will. He argued that God is too merciful to force his creatures to sin and then punish them and that He is too mighty to will a thing that would not transpire. In words of his successor al-Sadiq, God predestined some things but left others to man. Closely related is the early doctrine of , that is, advancement or postponement of an act of creation, depending on circumstances, without any change to the overall design and intention of God. The doctrine of thus describes an intermediate position between predestination and free will: God's decision on some matters remain suspended, according to al-Baqir, subject to advancement and postponement, until the autonomous choice of His creatures has occurred. Only then His definite decision is made. In turn, is closely tied to the concept of abrogation (nask (Tafsir)|) of some verses of the Quran.
Religious dissimulation () Muhammad al-Baqir is often credited with formulating the Shia doctrine of , that is, precautionary dissimulation to avoid persecution. was intended for the survival of Shia imams and their followers, for Shias were molested in al-Baqir's time to the point that he thought that it was easier to be a nonbeliever (zandaqa|). Traditions attributed to al-Baqir thus encourage his followers to hide their faith for their safety, some even characterising as a pillar of faith. For instance, al-Baqir is not known to have publicly reviled Abu Bakr and Umar, most likely because he exercised . Indeed, al-Baqir's conviction that the Islamic prophet had explicitly designated Ali ibn Abi Talib as his successor implies that Abu Bakr and Umar lacked legitimacy. Al-Baqir's quiescent views sharply differed from
Mu'tazilites, who held that
enjoining good and forbidding wrong should be enforced by force, if necessary. The notion of was not unfamiliar to early Muslims. When
Ammar, an early
companion of the Islamic prophet, renounced his faith under torture, Muhammad is said to have approved his conduct. The Quranic verse 16:106 is often connected to this episode. Other Quranic verses suggest that Abraham and
Joseph both practice dissimulation, the former when he said he was ill and the latter when his brother was accused of theft.
Religious dissociation () Al-Baqir also taught the doctrine of , that is, dissociation from the first three caliphs and the majority of the prophet's companions as enemies of Shia imams. Indeed, Imamites regard the early caliphs as usurpers of Ali's right to succeed the prophet.
Contributions to jurisprudence Al-Baqir founded what later developed into the Twelver school of law and consolidated some characteristic practices of the Shia. For instance, in the call to daily prayer (adhan|), al-Baqir added the expression (), an expression that was removed by Umar, according to Shia and some early Sunni sources. Al-Baqir also defended () marriage, saying that it was a practice sanctioned by the Islamic prophet, but later abandoned by Umar. In these rulings, al-Baqir thus sided with Ali ibn Abi Talib and
Ibn Abbas, two influential figures in early Islam. Another distinct ruling of al-Baqir was that wiping one's footwear before prayer, though common at the time, was unacceptable as a substitute for washing one's feet. Al-Baqir also forbade all intoxicants, whereas
Kufan jurists of his time permitted fermented drinks (). He also maintained that, under threat of death or injury, self-protection through dissimulation () is obligatory. Finally, is an extant treatise on the rituals of , attributed to al-Baqir and narrated by his disciple Abu al-Jurad Ziyad ibn Mundhir. Shia imams expected their disciples to seek (and then follow) their advice about new legal questions, or else answer those questions by applying limited reasoning within the general framework provided by imams. Al-Baqir is indeed known to have rebuked those who went beyond this framework, including Muhammad ibn al-Hakim and Muhammad al-Tayyar. In particular, al-Baqir discouraged his followers from (individual reasoning) or applying () and (). He considered these methods speculative and lacking in religious authority, which, in his view, was limited to Shia imams as the only authoritative interpretors of the Quran and the prophetic tradition (Sunnah|).
Contributions to Quranic exegesis Muhammad al-Baqir is credited with the Quranic exegesis :fa:تفسیر الباقر| (), narrated by his disciple Ibn al-Mundhir. Parts of this work have survived in Tafsir Qomi|, written by the Twelver scholar al-Qummi (). This commentary is ranked first by the Twelver bibliographer
al-Najashi () among early Quranic commentaries. Similarly, is a collection of exegetical traditions, ascribed to al-Baqir and narrated by his disciple
Jabir ibn Yazid al-Ju'fi. In , an extensive Twelver exegesis of the Quran, al-Baqir is the authority for thirteen percent of its traditions, behind only the prophet and al-Sadiq. == Notable disciples ==