Capture recapture is a method that involves estimating the number of cases in a defined population by crosslinking registrations of individual records of names. This study seeks to present the capture recapture technique as a more appropriate approach to use in estimating the number of population that are difficult to count. To illustrate the method, secondary data were obtained from three health facilities: Gembu Centre for HIV/AIDS Advocacy in Nigeria (GECHAAN), Mambilla Baptist Hospital (MBH), and General Hospital Gembu (GH) all located in Gembu, Taraba state and was used to estimate the prevalence of HIV in pregnant women from 2013 -2015. Log linear model was used to analyse the capture recapture data. Results show that the estimated completeness of the three sources was 14 % with the total prevalence of HIV in pregnant women estimated at 4372(95% CI [2274 -9767]), thus 3760were not registered by any of the three health facilities, since only 612 patients were identified by the centres. Validity of the results obtained was tested and was found to corroborate with the results obtained from existing alternative models. Result obtained shows that capture recapture technique has the ability to provide comprehensive data with a near accurate estimate.This method is useful for estimating elusive populationsas itis cost effective and an alternative to carrying out population based survey.