After his disqualification from the space program on medical grounds, he was an instructor at the cosmonaut training centre outside Moscow.

Varlamov showed great potential as a cosmonaut candidate, being physically fit and highly intelligent.

With the completion of the Vostok simulator, he was selected for a special group of six candidates for accelerated training, along with Yuri Gagarin, Anatoly Kartashov, Andrian Nikolayev, Pavel Popovich and Gherman Titov.

While on holiday in June that year with other cosmonaut candidates Georgy Shonin and Valery Bykovsky at Medvezh'i Ozyora (Bear Lakes) near Moscow, Varlamov suffered a neck injury after diving into shallow water.

"[5] He continued to work within various departments of the cosmonaut training centre and was promoted to major in 1964, followed by lieutenant colonel in 1968.