Abstract: A method of simultaneously estimating a diplotype-based penetrance as well as haplotype frequencies and diplotype configurations on the basis of observed genotype and phenotype data. The method includes a step a of calculating, on the basis of genotype data and phenotype data with haplotype frequencies and penetrance used as parameters, the maximum likelihood (L0max) obtained by maximizing likelihood under the hypothesis that there is no association between predetermined diplotype configurations and a predetermined phenotype, the maximum likelihood estimates of haplotype frequencies and penetrances, the maximum likelihood (Lmax) obtained by maximizing likelihood under the hypothesis that there is an association between the predetermined diplotype configurations and the predetermined phenotype; and a step b of calculating the penetrance from the maximum likelihood estimate obtained in said step a.