OBJECTIVE: To introduce the approaches for estimating gene-environment interaction based on partial case-control studies. METHODS: The effects of logistic model and log-linear model for estimating the main effects and gene-environment interaction effect were estimated by means of maximum likelihood methods in traditional case-control studies, case-only studies and partial case-control studies, respectively. An example was also illustrated. RESULTS: In traditional case-control study with complete data, the results of logistic model and log-linear model were equivalent. In case-only study without any information about controls, the logistic model can also efficiently estimate gene-environment interaction. In partial case-control study, environmental information was collected from all of the cases and controls, while genetic information was only collected from cases. For this case-control study with incomplete data, a suitable parameterized log-linear model could simultaneously and efficiently estimate the main effect of environment and gene-environment interaction, whereas the logistic model could not. CONCLUSION: For a partial case-control study, log-linear model could estimate not only the main effect of environment but also gene-environment interaction. If genotype and exposure were independent, estimators from partial case-control were as precisely as those from complete-data case-control studies.