Circular plasmids containing an autonomously replicating sequence (ARS) and a centromeric DNA sequence (CEN) segregate as independent linkage groups during meiosis in Saccharomyces cerevisiae. If two genetically marked plasmids are present in the same diploid cell, their segregation during meiosis may be determined relative to each other. It has been observed that for centromere plasmids containing some DNA sequences in common, these plasmids tend to segregate away from each other at the first meiotic division [Clarke, L. & Carbon, J. (1980) Nature (London) 287, 504-509; Clarke, L., Fitzgerald-Hayes, M., Buhler, J.-M. & Carbon, J. (1981) Stadler Genet. Symp. 13, 9-23]. Here we show that nonhomologous plasmids, having no detectable DNA sequence cross-hybridization, also tend to disjoin from each other at the first meiotic division. Therefore, this nonrandom segregation to opposite poles can occur by mechanisms that do not involve DNA sequence homology. This process may be an active nonhomologous pairing system or it may reflect unknown physical restraints on the meiotic segregation of the two plasmids. In either case, this process cannot be used as a possible assay for homologous meiotic pairing.