Incompatible nuclear-cytoplasmic interactions are responsible for the phenomenon of cytoplasmic male sterility in plants. We have analysed male sterile (2077A, 296A), maintainer fertile (2077B, 296B) and fertility restored (2077R, 296R) lines of sorghum for the restriction fragment locations of various mitochondrial genes and their transcripts. We report here a polymorphism in genes related to the ATP synthase complex between two different cytoplasms from the A and B set of lines of 2077 and 296. There is also a difference in the transcript size of theatpA gene between the A and B cytoplasms. We propose that incompatibility in nuclear cytoplasmic interactions may be explained in terms of incompatible subunits being synthesized by the mitochondria and nucleus for a multisubunit complex of the mitochondrial membrane such as ATPase.