Several natural variants of mouse hepatitis viruses have been compared by the T1-oligonucleotide fingerprinting technique. In general, they have diverged quite extensively. However, MHV-3, a hepatotropic strain, and A59, a nonpathogenic strain, were found to be extremely related. Yet, each of them contains 2-4 specific oligonucleotides. One of the MHV-3-specific oligonucleotides was mapped in 30S poly(A)-containing RNA or 6-7 Kb from the 3-end and the other near the 5'-end of the genome. These two genetic regions might be associated with viral pathogenicity. In addition, two JHM plaque variants, DL producing large plaques and DS producing small plaques, were also compared. They share almost all T1-oligonucleotides, but each contains one unique spot. The DL-specific oligonucleotide was mapped in 21S poly(A)-containing RNA or at about 4 kb from the 3'-end. Finally, the MHV genome was found to contain the "cap" structure, confirming that it is a positive-stranded RNA.