"The disease of secularitis has spread in Indian politics. Just like encephalitis, secularitis is very dangerous," he said here.
The comment comes as questions continue to be raised on the secular credentials of Gujarat Chief Minister Narendra Modi - the party's poll campaign committee chief who has emerged as a strong contender for the prime minister's post.
Modi has been accused of involvement in the 2002 post-Godhra riots in Gujarat.
Rajnath Singh also took a dig at Congress general secretary Shakeel Ahmad who July 21 said that terror module Indian Mujahideen was formed after the 2002 Gujarat riots.
"He says Indian Mujahideen (IM) was formed after the Gujarat riots, I would say this Congress leader (Ahmad) has the horoscope of IM. Whoever needs any detail about the IM can go to the Congress headquarters and meet this leader," he said.
"As if there have been no riots in independent India before the 2002 one," Rajnath Singh said.