The application of multiway contingency table analysis to the multivariate analysis of concordance ratios in twin studies is developed. The approach is illustrated by data on smoking and alcohol use in Finland and Sweden. This approach can enable the assessment of the effect of other variables on the concordance ratio and thus allow estimates of genetic effects on the trait under study. Hypotheses on relationships between genetic effects and other variables can be tested. After hypothesis testing, model fitting of the best hypothesis can be carried out.