Varghese’s only son Thomas was born on the 25th July 1947. A B.Sc. graduate, Thomas 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. Ivin Joseph and Dr. Joe Varghese and a daughter, Dr. Shobha.