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An ethnographic pre-assessment study of the behavioral dynamics of men who have sex with men (MSM) and injecting drug users (IDU) was conducted in 2009 as an integral part of the 2010 Integrated Biological and Behavioural Surveillance Survey (IBBSS). The study took place in Northern and Southern Nigeria and provided rich contextual information on the logistic and scientific factors that would aid successful conduct of the IBBSS and secure buy-in for it among study respondents. The study utilized a combination of rapid assessment procedures that were suitable to prevailing time exigencies and could foster preliminary understanding of the local contexts of risk behaviors of IDU and MSM. Its data reinforce the status of IDU and MSM as significant risk communities in the six states of Nigeria. This report details overall results showing that logistical and technical aspects are important for the conduct of the 2010 IBBSS. Logistical issues include how and when to recruit respondents; confidentiality issues; decisions about venues; objective recruitment of fieldworkers; review of the incentive system for respondents; and provision of adequate security.