ABSTRACT: Introduction: This paper details the methods used in the second national Biological and Behavioral Surveillance Survey (BBSS) of HIV, syphilis, and hepatitis B and C among men who have sex with men in Brazil. Methods: Respondent-driven sampling (RDS) was used in 12 cities in 2016. The targeted sample size was initiated with five to six seeds in each city. HIV, syphilis, and Hepatitis B and C rapid tests were offered to participants. RDS Analyst with Gile’s successive sampling (SS) estimator was used to adjust results as recommended and a weight for each individual was generated for further analysis. Data for the 12 cities were merged and analyzed using Stata 14.0 complex survey data tools with each city treated as its own stratum. Results: Duration of data collection varied from 5.9 to 17.6 weeks. 4,176 men were recruited in the 12 cities. Two sites failed to achieve targeted sample size due to a six-month delay in local IRB approval. No city failed to reach convergence in our major outcome variable (HIV). Conclusion: The comprehensive BBSS was completed as planned and on budget. The description of methods here is more detailed than usual, due to new diagnostic tools and requirements of the new STROBE-RDS guidelines.