The stratification score for a case-control study is the probability of disease modeled as a function of potential confounders. The authors show that the stratification score is a retrospective balancing score and thus plays a similar role in case-control studies as the propensity score plays in prospective studies. The authors further show how standardization using the stratification score can be used to compare the distributions of exposures that would be found among case and control participants if both groups had the same distribution of confounding covariables. The authors illustrate these results using data from a genome-wide association study, the GAIN (Genetic Association Information Network) study of schizophrenia among African Americans (2006-2008).