Cultural neuroscience is an emerging research discipline that investigates cultural variation in psychological, neural and genomic processes as a means of articulating the bidirectional relationship of these processes and their emergent properties. Research in cultural neuroscience integrates theory and methods from anthropology, cultural psychology, neuroscience and neurogenetics. Here, we review a set of core theoretical and methodological challenges facing researchers when planning and conducting cultural neuroscience studies, and provide suggestions for overcoming these challenges. In particular, we focus on the problems of defining culture and culturally appropriate experimental tasks, comparing neuroimaging data acquired from different populations and scanner sites and identifying functional genetic polymorphisms relevant to culture. Implications of cultural neuroscience research for addressing current issues in population health disparities are discussed.