BACKGROUND: Some reports suggest there are differences in health needs between the population affiliated to the subsidized health insurance scheme (SS) and those affiliated to the contributory health insurance scheme (CS) in Colombia. The objective of this study was to identify the epidemiological profile of the population affiliated to the SS in Colombia and to compare the main epidemiological features of the SS to the CS. METHODS: Following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) methodology, the search was carried out from 1993, with no other restriction. The information was synthesized into five categories according to the most important risk populations. We estimated combined incidences from epidemiological surveillance data, prevalence ratio, and other measures to estimate the difference between the studied groups. A 95% confidence interval was considered. A random effects model was used weighted by the inverse of the variance of the cumulative incidence calculated for each disease. The risk of bias was assessed using the Joanna Briggs Institute's critical appraisal tools. RESULTS: A total of 16,236 articles were identified; 14,972 were excluded after title and abstract screening, 725 articles were verified as full text, and finally 268 articles were included. The relative risk of non-communicable and communicable diseases was lower in the SS than in the CS (RR: 0.37 and 0.72, respectively, p-value < 0.05). However, the risk of presenting obstetric and maternal conditions in the SS versus the CS was RR 1.55 for frequent conditions during early childhood, and for other diseases it was RR 1.28 with a p-value of < 0.05. The use of health services was different by scheme, with less demand, access, and provision being found in health services in the SS. CONCLUSIONS: This study allowed us to conclude that there are differences in the incidence, prevalence, and use of health services between health affiliation schemes (SS and CS) in Colombia, thereby assisting in decision-making for stakeholders. TRIAL REGISTRATION: PROSPERO Registration number CRD42021279234.