Borodin was born Mikhail Markovich Gruzenberg () to a Jewish family in Yanovichi, Russian Empire, now part of Vitebsk Region, Belarus, on 9 July 1884. At a very young age, he began work as a boatman on the Western Dvina, traversing the stretch of the river between Vitebsk, Dvinsk, and Riga, now the capital of Latvia. He later moved to Riga, where he attended Russian-language night schools while working in the city's port. He joined the General Jewish Labour Bund at age sixteen, switching allegiance to Vladimir Lenin's Bolsheviks in 1903. He became a close associate of Lenin, making use of his knowledge of the Yiddish, German, and Latvian languages in work as a Bolshevik agent in the empire's northwest region. In mid-1904, he was ordered to travel to Switzerland to meet Lenin, who had gone into exile. Following the "Bloody Sunday" massacre of unarmed protesters by Tsarist troops in Saint Petersburg on 9 January 1905, Borodin returned to Russia, organised revolutionary activity in Riga, and was later selected to attend the Bolshevik conference at Tampere, where he met Joseph Stalin.