The technique of oligonucleotide fingerprinting is a useful tool for analyzing sequence homology among RNA molecules. A rapid method for the simultaneous production of multiple fingerprints has been developed using a commercially available electrophoresis apparatus. The system makes use of relatively small gels, yielding fingerprints that when compared to conventional systems are of reduced size but of comparable resolution. The system described should have particular application to the analysis of RNA viruses with multiple genome segments, and in epidemiologic studies concerned with the analysis of multiple virus isolates.