We report the application of a highly sensitive column chromatographic technique to the comparison of tryptic peptide maps of some RNA tumor virus proteins. By combining microbore ion-exchange chromatography with a sensitive fluorescent assay using o-phthalaldehyde, we obtained high-resolution peptide maps starting with only microgram amounts of protein. Our discovery of coincident peptides from the 15,000 and 30,000 molecular weight proteins from murine and feline leukemia viruses supports serological evidence for interspecies antigenic determinants; coincident peptides were also found for the 10,000 molecular weight proteins from these viruses, although immunochemical data did not reveal interspecies determinants. The relatively large number of coeluting peptides found in the 15,000 and 10,000 molecular weight proteins is strong evidence for the existence of homology.