The general method of segregation analysis of pedigree data has been developed and widely used in human genetics. We modified this method to examine pedigree data coming from inter-population crosses. These kinds of pedigrees are common in laboratory and farm animal breeding. This paper describes a rationale for the method and illustrates its application to the study of inheritance of litter size and of male sterility in hybrid stock of the house musk shrew (Suncus murinus) derived from crosses of two geographically isolated populations.