National surveillance of tuberculosis cases is based on the mandatory reporting system (DO). In 1992–1993, an estimate of the completeness of mandatory reporting for this disease was conducted using the capture-recapture method on a sample of 15 departments. It estimated the system’s completeness at 43%. The objective of this study was to track changes in the surveillance system by conducting a new assessment of its completeness using the same method and analyzing its characteristics for the entire Rhône-Alpes region. The three-source capture-recapture method was applied using log-linear models and accounting for heterogeneity variables for all diagnosed cases and for the subset of bacteriologically confirmed cases due to differences in case definitions among the three sources. This method made it possible to estimate the total number of cases and the completeness of each of the three data sources. To do this, a retrospective collection of tuberculosis cases leading to exemption from the patient copayment was conducted with the medical departments of the health insurance funds (CAM), as well as a collection of cases identified from all public and private clinical laboratories. These data were cross-referenced with cases reported to the DDASS. After eliminating duplicates, a total of 1,306 cases of diagnosed tuberculosis and 947 bacteriologically positive cases were identified. According to the best log-linear model, which included interactions between the DO and CAM sources and between DO and LABM, the total estimate of the number of diagnosed cases was 1,767 cases. The completeness of the DO, likely underestimated due to differences in case definitions across sources, was 44% [41–49]. For cases with pulmonary involvement, it was 51% [47–55] and was higher in the most populous departments, reaching 65% [56–77] in the Rhône. For bacteriologically confirmed cases, the estimated number of cases according to the best model accounting for an interaction between the DO and CAM sources was 1,122 [1,077–1,167] cases, and the completeness of the DO reached 54% [52–56]. This completeness varied by geographic area in the same way as in the analysis of all cases. The analysis of bacteriologically confirmed cases was more reliable, as the case definition was identical for all three sources. The results showed that DO completeness remained generally poor, with no significant change since the first study conducted in 1992–1993. The observed correlation between geographic area and reporting completeness suggested that mandatory reporting varied according to area-specific characteristics (urbanization, healthcare availability). These factors could help guide new awareness-raising initiatives. The inclusion of laboratory directors as reporting entities should be evaluated in the future as a factor in improving reporting of this disease, particularly regarding bacteriologically confirmed cases.