This study evaluates the level of underreporting of the National Program of Leishmaniasis Control (NPLC) in two communities of Cochabamba, Bolivia during the period 2013-2014. Montenegro skin test-confirmed cases of cutaneous leishmaniasis (CL) were identified through active surveillance during medical campaigns. These cases were compared with those registered in the NPLC by passive surveillance. After matching and cleaning data from the two sources, the total number of cases and the level of underreporting of the National Program were calculated using the capture-recapture analysis. This estimated that 86 cases of CL (95% confidence interval [CI]: 62.1-110.8) occurred in the study period in both communities. The level of underreporting of the NPLC in these communities was very high: 73.4% (95% CI: 63.1-81.5%). These results can be explained by the inaccessibility of health services and centralization of the NPLC activities. This information is important to establish priorities among policy-makers and funding organizations as well as implementing adequate intervention plans.