OBJECTIVES: Gene-environment (GxE) interaction influences risk for many complex disease traits. However, genome screens using affected sib pair linkage techniques are typically conducted without regard for GxE interaction. We propose a simple extension of the commonly used mean test and evaluate its power for several forms of GxE interaction. METHODS: We compute expected IBD sharing by sibling exposure profile, that is by whether two sibs are exposed (EE), unexposed (UU), or are discordant for exposure (EU). We describe a simple extension of the mean test, the "mean-interaction" test that utilizes heterogeneity in IBD sharing across EE, EU, and UU sib pairs in a test for linkage. RESULTS: The mean-interaction test provides greater power than the mean test for detecting linkage in the presence of moderate or strong GxE interaction, typically when the interaction relative risk (R(ge)) exceeds 3 or is less than 1/3. In the presence of strong interaction (R(ge) = 10), the required number of affected sib pairs to achieve 80% power for detecting linkage is approximately 30% higher when the environmental factor is ignored in the mean test, than when it is utilized in the mean-interaction test. CONCLUSION: Linkage methods that incorporate environmental data and allow for interaction can lead to increased power for localizing a disease gene involved in a GxE interaction. Copyright 2001 S. Karger AG, Basel