The protein product of the mouse preimplantation embryo development (Ped) gene, which controls the rate of preimplantation embryonic cleavage division and subsequent embryo survival, is the Qa-2 antigen. This major histocompatibility complex (MHC) class I b protein is encoded by four genes, Q6, Q7, Q8, and Q9. The present study was undertaken to begin to elucidate which of the four Qa-2-encoding genes are responsible for the Ped gene phenotype in the C57BL/6 mouse (H2(b)). First, restriction maps of the four genes, using 25 restriction enzymes, were created. The RE maps confirmed that Q6 is similar to Q8 and Q7 is similar to Q9, but that the Q6/Q8 gene pair differs from the Q7/Q9 gene pair. The genomic DNA sequences of Q6 and Q8 were determined, as well as the DNA sequences of exons 4 - 8 of Q9, and the 5' regulatory regions of Q6, Q8, and Q9. This DNA sequence information, combined with the published DNA sequence information for the entire Q7 gene and exons 1 - 3 of Q9, allowed us to design primers for reverse transcription-polymerase chain reaction that could distinguish which of the four genes were transcribed in mouse lymphocytes and embryos. It was found that all four genes are transcribed in lymphocytes, but only Q7 and Q9 are transcribed in mouse embryos. Thus, both Q7 and Q9 are candidates for the genes responsible for the Ped gene phenotype.