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Background: This paper aims to instigate discussion and publication of methodologies applied to enhance quality management through comprehensive scientific reports. It provides a detailed description of the design, implementation, and results of the quality control program employed in the SMESH study., Methods: Cross-sectional, multicenter, national study designed to assess the prevalence of human papillomavirus in sex workers and in men who have sex with men (MSM). Respondent-driven sampling recruitment was used. An online system was developed for the study and checkpoints were defined for data entry. The system checked the quality of biological samples and performed a retest with part of the sample., Results: A total of 1.598 participants (442 sex workers and 1.156 MSM) were included. Fifty-four health professionals were trained for face-to-face data collection. The retest showed Kappa values ranging between 0.3030 and 0.7663., Conclusion: The retest data were mostly classified as indicating a strong association. The data generated by the checkpoints showed the successful implementation of the quality control program., (© 2024. The Author(s).)