Shafarevich came into conflict with the Soviet authorities in the early 1950s but was protected by Ivan Petrovsky, the Rector of Moscow University.

He compared Thomas More's (Utopia) and Tommaso Campanella's (City of the Sun) visions with what is known about the Inca Empire and concluded that there are striking similarities.

He claimed that we become persons through our relationship with God and argued that socialism is essentially nihilistic and is unconsciously motivated by a death instinct.

Shafarevich adhered to Russian Orthodox Christianity and incorporated the neo-Platonic views of Eastern Orthodoxy into his understanding of the relation of mathematics and religion.

[9] In his talk to the Göttingen Academy of Sciences upon receiving a prize, Shafarevich presented his view of the relationship between mathematics and religion.

[10] Defunct On 21 December 1991 he took part in the first congress of the Russian All-People's Union, headed by Sergei Baburin.

Shafarevich's essay Russophobia[11] was expanded into his book Three Thousand-Year-Old Mystery (Трехтысячелетняя загадка) and resulted in accusations of antisemitism.

At the same time, Shafarevich condemned the methods that were used to screen out applicants of Jewish origin when entering prestigious Moscow universities in the 1970s and early 1980s.

In Shafarevich's opinion, the role of such a 'small nation' in Russia was played by a small group of intelligentsiya, dominated by Jews, "who were full of hatred against traditional Russian way of life and played an active role in the terrorist regimes of Vladimir Lenin and Joseph Stalin".

[23] Semyon Reznik targets the Russophobia essay for factual inaccuracies: Shafarevich misassigned Jewish ethnicity to a number of non-Jews involved in the execution of Nicholas II, repeated the false assertion of graffiti in Yiddish at the murder site and suggested that Shafarevich's phrase "Nicholas II was shot specifically as the Tsar, and this ritual act drew a line under an epoch in Russian history" – is read by some as a blood libel.

[16] (An accusation which ignores the remainder of Shafarevich's sentence: "so it can only be compared with the execution of Charles I in England or of Louis XVI in France".

[24] Later, Shafarevich expanded on his views in his book Three Thousand-Year-Old Mystery in which he further claimed that Jews effectively marginalise and exclude non-Jews in all types of intellectual endeavors.