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This paper presents key methodological approaches and challenges in implementing and analysing the first round of the integrated biobehavioural assessment of most-at-risk populations, conducted in conjunction with evaluation of Avahan, the India AIDS initiative.The survey collected data on HIV risk behaviours, sexually transmitted infections and HIV prevalence in 29 districts in six high-prevalence states of India. Groups included female sex workers and clients, men who have sex with men, injecting drug users and truck drivers. Strategies for overcoming some challenges of the large-scale surveys among vulnerable populations, including sampling hidden populations, involvement of the communities targeted by the survey, laboratory and quality control in remote, non-clinic field settings, and data analysis and data use are presented.Satisfying the need for protocols, guidelines and tools that allowed for sufficient standardization, while being tailored enough to fit diverse local situations on such a large scale, with so many implementing partners, emerged as a major management challenge. A major lesson from the first round is the vital importance of investing upfront time in tailoring the sampling methods, data collection instruments, and analysis plan to match measurement objectives.Despite the challenges, the integrated biobehavioural assessment was a huge achievement, and was largely successful in providing previously unavailable information about the HIV situation among populations that are critical to the curtailment of HIV spread in India. Lessons from the first round will be used to evolve the second round into an exercise with increased evaluative capability for Avahan.