The Hedgewar home was also the venue of the first ever meeting of the RSS which he founded in September 1925.
Accorded a warm welcome at the RSS headquarters, Mukherjee was shown around the Hedgewar memorial premises which includes a small temple.
His visit has raised many an eyebrow, including in his own party.
The RSS was banned on February 4, 1948 following the assassination of Mahatma Gandhi. The ban was lifted on July 11, 1949 after then Sarsanghchalak M.S. Golwalkar gave an undertaking that the organisation would abide by the Indian Constitution.
Brushing aside all criticism, the former President arrived here on Wednesday evening with the main engagement being the RSS function at Reshim Baug.
He was received at the airport by RSS functionaries, but there was nobody from the Congress - the party with which he was associated for several decades before he became the 13th President of India in 2012.
In view of a heavily overcast weather in the Orange City, alternative arrangements have been made at a nearby closed door auditorium in case it starts raining.
According to present indications, Mukherjee will address the RSS gathering for around 20 minutes and later have dinner with the RSS leaders before departing from Reshim Baug late on Thursday.
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