Context: Chronic disease, a global burden, puts patients in increased and prolonged need of care. Adequate and reliable information on chronic diseases is necessary for the implementation of health policies. Aim: The aim is to study the epidemiological characteristics of chronic diseases that exist in Benin and the Ouémé department and to compare the prevalence of chronic diseases identified in urban areas with those of the rural areas in this department. Settings and design: This is a comparative cross-sectional study. Materials and Methods: The study was conducted using a chronic disease identification sheet, the Delphi method, interview and analysis of consultation records. Statistical analysis used: The data collected with the questionnaire were processed with the SPSS software (IBM, version 21.0). The information collected during the interviews was processed by content analysis in three parts: information condensation, coding, analysis and interpretation of the results. Results: The study participants were active, married and aged 31 to 60. High blood pressure, diabetes, sickle cell disease, SS and SC, peptic ulcer disease, hepatitis B and C, sinusitis, asthma and AIDS have been identified, both in urban and rural areas. Considering the eight identical diseases in both settings, the highest prevalence in urban areas is diabetes, while, hypertension in rural areas. The lowest prevalence is that of AIDS, whether in urban or rural areas. Conclusion: The data from this study constitute a database for the definition of policies and strategies for the management of people with chronic diseases.