Varghese’s only son Thomas is a B.Sc. graduate and has worked in many foreign countries. Now he is a Training and Development specialist at the Emirates Airline Staff Training College in Dubai. Kunnamkulam Paramel Itoop’s daughter, Dr. Annie Susan (Unnikutty) is his wife. Dr. Annie is an official in the Health Ministry of Ras-Al-Khaimah. They have two sons, Dr. Joseph Ivin and Dr. Joe Varghese and a daughter, Dr.Shoba.