Interactions between genetic and early environmental factors are recognized to play a critical role in modulating susceptibility to disease, particularly mental illness. In order to better understand such mechanisms at the molecular level, we have developed a screening paradigm in mice that allows us to test the ability of targeted mutations in candidate genes to modify susceptibility to the long-term effects of different maternal environment. Offspring of genetically identical F1 hybrid dams produced by reciprocal breeding of C57BL/6 and BALB/c parents show alterations in anxiety-related behavior as a consequence of their different maternal environment. Introduction of targeted mutations into these offspring via the father allows for the identification of candidate genes that alter these maternal effects. Our strategy offers several advantages over other methods to study maternal effects, including the use of genetically identical parents, the ability to identify both prenatal and postnatal effects, the straightforward introduction of mutations and its adaptability to high-throughput screening. In order to test the utility of this paradigm to screen candidate genes, we tested for gene-environment interactions involving loss-of-function mutations in the serotonin 1A receptor gene. Our studies demonstrate that early gene-environment interactions can be successfully tested in the mouse. When combined with conditional gene targeting and other molecular genetic techniques available in the mouse, this approach has the potential to identify the molecular mechanisms underlying early gene-environment effects.