Identifying population stratification and genotyping error are important for candidate gene association studies using the Transmission Disequilibrium Test (TDT). Although the TDT retains the prespecified Type I error in the presence of population stratification; the test may have decreased power in the presence of population stratification. Genotyping error can also cause the TDT to have an elevated Type I error. Differentiating population stratification from genotyping error remains a challenge for geneticists. Both genotyping error and population stratification can result in an increase in the observed homozygosity of a sample relative to that expected assuming Hardy-Weinberg Equilibrium (HWE). We show that when family data are available; even if a limited number of markers are genotyped; evaluating the markers that show statistically significant deviation from HWE with the Mating Type Distortion Test (MTDT) – a test based on the mating type distribution – can reliably differentiate genotyping error from population stratification. We simulate data based on several models of genotyping error in previously published literature; and show how this method could be used in practice to assist in differentiating population stratification from systematic genotyping error.