Objectives Resource-limited countries often lack robust routine surveillance systems to accurately assess the burden of human attributes and diseases. In these settings capture-recapture analysis can be an alternative tool to obtain prevalence and incidence rates. Performance of capture-recapture analyses in resource-limited countries has not been systematically reviewed. Methods Systematic review of the performance of capture-recapture analyses in the categories of human attributes, non-infectious and infectious diseases in resource-limited countries, assessing individual study quality criteria and a minimum quality criterion per category, using PRISMA methodology. Results A total of 1671 potentially relevant PubMed citations were screened, resulting in 52 eligible publications: 36% in human attributes, i.e. hidden populations, injuries and mortality; 48% in non-infectious and 15% in infectious disease categories. Twenty-one per cent of selected studies were from low income countries, 40% from lower-middle-income countries and 38% from upper-middle-income countries. Thirteen per cent achieved good individual study quality criteria, 25% were intermediate and 19% were poor. Of the good studies, six were performed on human attributes and one on a non-infectious disease. The proportions of publications meeting the minimum quality criterion per category were 42%, 20% and 37%, respectively. Conclusions Few capture-recapture studies in resource-limited countries achieved good individual quality criteria and a minority met the minimum quality criterion per category. Capture-recapture techniques in these settings should be carefully considered and implemented rigorously and are not a panacea for strengthening of routine surveillance systems.