Community Health Insurance (CHI) in Uganda faces low enrolment despite interest by the Ugandan health sector to have CHI as an elaborate health sector financing mechanism. User fees have been abolished in all government facilities and CHI in Uganda is limited to the private not for profit sub-sector, mainly church-related rural hospitals. In this study, the reasons for the low enrolment are investigated in two different models of CHI. Focus group discussions and in-depth interviews were carried out with members and non-members of CHI schemes in order to acquire more insight and understanding in people's perception of CHI, in their reasons for joining and not joining and in the possibilities they see to increase enrolment. This study, which is unprecedented in East Africa, clearly points to a mixed understanding on the basic principles of CHI and on the routine functioning of the schemes. The lack of good information is mentioned by many. Problems in ability to pay the premium, poor quality of health care, the rigid design in terms of enrolment requirements and problems of trust are other important reasons for people not to join. Our findings are grossly in line with the results of similar studies conducted in West Africa even if a number of context-specific issues have been identified. The study provides relevant elements for the design of a national policy on CHI in Uganda and other sub-Saharan countries.