The objective of the study was to estimate the population of HIV-seropositive pregnant women in the State of Sergipe between 2000 and 2010, using the capture-recapture method (CRC). Three databases were used as independent lists: The Brazilian Case Registry Database (SINAN), Laboratory Test Control System (SISCEL) and medical data records of the STD/HIV/AIDS service of Sergipe (CEMAR). For analysis, a log-linear regression model was used to ascertain the total population size. We identified 729 HIV-seropositive pregnant women from the three lists. Among them, only 317 (43.5%) were included in SINAN, 646 (88.6%) were included in SISCEL and 274 (37.6%) appeared in the CEMAR database. Using CRC, we estimated that there were in total 1110 HIV-seropositive pregnant women; therefore, 381 (34.3%) women were not captured by any of the three systems. The CRC method is a potentially useful and important tool in the evaluation of official reporting systems in Brazil.