Maternally transmitted antigen (Mta) is a murine cell surface class I-like antigen that is defined by specific cytotoxic lymphocyte reactivity. Mta is unique in that its expression requires cooperation between genetic elements both in the Qa/Tla region of chromosome 17 and in the cytoplasm. In view of the known cytoplasmic, and thus maternal, inheritance of mitochondria, we have directly assessed their potential involvement in Mta expression. The mitochondria-specific lethal dye rhodamine 6G (R6G) was used to control the input of mitochondria into cell hybrids. The parental lines, one of BALB/c and one of NZB origin, were known to differ in Mta and mtDNA phenotype. Our data show that most control BALB/c-NZB hybrids expressed the BALB/c Mta phenotype and likewise contained only BALB/c-type mtDNA. The NZB Mta phenotype was not coexpressed in the control hybrids. However, when the mitochondrial contribution from BALB/c was prevented by R6G treatment, the majority of the resultant hybrids expressed only the NZB Mta type and likewise contained only NZB mtDNA. The exceptional R6G-treated hybrids that continued to express the BALB/c Mta phenotype likewise contained only BALB/c mtDNA. Thus, in every case the mtDNA phenotype correlated with the Mta phenotype of the cells. Together, the data support the remarkable conclusion that mitochondria modulate the phenotypic expression of a cell surface molecule.