Missing genotype data arise in association studies when the single-nucleotide polymorphisms (SNPs) on the genotyping platform are not assayed successfully, when the SNPs of interest are not on the platform, or when total sequence variation is determined only on a small fraction of individuals. We present a simple and flexible likelihood framework to study SNP-disease associations with such missing genotype data. Our likelihood makes full use of all available data in case-control studies and reference panels (e.g., the HapMap), and it properly accounts for the biased nature of the case-control sampling as well as the uncertainty in inferring unknown variants. The corresponding maximum-likelihood estimators for genetic effects and gene-environment interactions are unbiased and statistically efficient. We developed fast and stable numerical algorithms to calculate the maximum-likelihood estimators and their variances, and we implemented these algorithms in a freely available computer program. Simulation studies demonstrated that the new approach is more powerful than existing methods while providing accurate control of the type I error. An application to a case-control study on rheumatoid arthritis revealed several loci that deserve further investigations.