At the age of 18, after his FA examinations, Iyer's parents conducted his marriage with 9 year old Akilandam, who remained his spouse for the rest of his life.
[4][5] On 8 July 1939, Vaidyanatha Iyer entered the Meenakshi temple at Madurai in the company of L. N. Gopalasamy and six of his Dalit friends, P. Kakkan, Muruganandam, Chinniah, Purnalingam and Muthu.
[9] The Tamil Nadu Harijan Sevak Sangh wrote a biography in honor of Iyer that was named “Harijana Thanthai Amarar Vaidyanatha Iyerin Vazhkai Varalaaru (Biography of the Immortal Vaidyanatha Iyer, Father to all Harijans)”.
Every year, on Iyer's death anniversary (February 23), people pay respect to him by garlanding a statue of him.
Every year on that day, respects are paid to his memorial at the Chennai Thakkar Baba Vidyalaya School and the Madurai ‘Sevalayam’, which was started by Iyer in 1932 to serve Harijans.