AbstractStimulated by a large pedigree with a cochlear form of deafness, for which we considered a two‐locus mitochondrial and nuclear gene model, we have extended the classic methods of segregation analysis to these classes of two‐locus disorders. Based on the unique maternal transmission pattern of the mitochondria, we demonstrate that utilization of the maternal line pedigree allows us to simplify the various two‐locus mitochondrial models to ‘one nuclear locus’ models. Classifying the nuclear families into different independent groups by the mother's phenotypes allows us to estimate the nuclear gene frequency in one group and to use this estimate as the expected value to test the fitness of the model on the other group. In addition, if we restrict the analysis to specific subsets of the mating type(s), we can also test the model on specific groups of nuclear families without estimating the gene frequency. Goodness‐of‐fit tests can be performed on pooled sibship data as well as individual sibship data. These methods of analysis should assume increasing importance as more disorders with features of mitochondrial inheritance are identified. © 1992 W