Epilepsy is a devastating neurological disorder in which those afflicted can gain benefit from specific treatments based on their genetics and geographic location. Currently the prevalence of epilepsy is estimated at 0.5-3% of the world-wide population, and is increasing in developing countries. In order to make more accurate assessments of the prevalence of epilepsy, we applied the capture-recapture method in a 12-month study of epilepsy in a population from the Sharur district of Nakhichevan Autonomous Republic, Azerbaijan with 114,451 people from sixty nine villages and towns. The following methods were applied to determine epilepsy: Door To Door (DTD) survey, Non-Medical Source (NMS), and Medical Source. Using these three techniques, 1,032 patients with epilepsy (9.02/1000) were included in our study. The DTD survey determined 627 patients with epilepsy (5.48/1000) and 247 (2.16/1000) from the NMS methods versus 158 (1.38/1000) from the Medical Source (MS) methods. Applying the capture-recapture method, NMS, and DTD methods, the number of epilepsy cases increased to 1,330 (11.62/1000) [95% CI: 10.21-13.03]. The combinations of these methods show that 887 people (7.75/1000) have a diagnosis of epilepsy. Multiple epidemiological tasks used in our study can be used to estimate clinical signs and/or markers in future applications for the determination and development of treatment strategies for this devastating disease in the third world countries such as the Nakhichevan Autonomous Republic of Azerbaijan.