This report aims to summarize the Think Tank discussions, focusing on contemporary analysis of GxE interactions for cancer and other complex diseases. Specifically, we provide an overview of motivation for performing GxE analysis, present methods that can be applied to existing genetic and exposure data within observational studies to characterize and discover GxE interactions, discuss key considerations for analysis in case-control or nested case-control studies, and comment on interpretation of GxE interactions. We highlight some key unanswered questions (Box 1).