This paper is about health and biosocial processes at Eid-Babiker Qur’anic School (khalwa). It aims at investigating the health and social problems of students aged (10-15) years, studying Quran and Islamic education. A mix-method consisting of quantitative and qualitative tools of data collection was implemented to collect data whereby a random sample of 200 students were clinically examined to investigate the prevalence of diseases among them. As well focus group discussion and interviews were conducted with students and key persons in the Khalwa to explore the mechanisms of running it and process of dealing with emerging social and health challenges. The results reflect that students were proved to be infected with schistosomiasis and some other fungal diseases. About 47% of those who were examined were suffering malnourishment-related problems such as anaemia. Health education is not reinforced however the students reflect collective identity and team work spirit, which is operating outside the context of the community outside the Khalwa. It is highly recommended that health care should be given attention it might be important to consider to establish a small health care unit.