We have cloned the Caenorhabditis elegans sex determining gene, tra-2, by transposon tagging. The tra-2 region is delineated by mapping Southern blot differences associated with 11 tra-2 mutations, mutant rescue, and analysis of tra-2 RNAs. The tra-2 gene encodes three transcripts. One transcript, a 1.8 kb RNA, is not detected in animals lacking a germ line, and therefore may be germline specific. Comparison of the two sexes shows that adult hermaphrodites have approximately 15-fold more tra-2 RNA than adult males. In addition, adult hermaphrodites contain 5 kb and 1.8 kb tra-2 RNAs whereas adult males possess 5 kb and 1.9 kb RNAs. A 1.9 kb tra-2 RNA is also found during hermaphrodite larval development, prior to sexual differentiation of the XX germ line. Surprisingly, analysis of tra-2 expression in selected sex determination mutants reveals that the sex specificity of tra-2 RNAs is not dictated by the pathway of sex determination that has been established by genetic experiments. This result can be interpreted in two ways. Either the sex specificity of the tra-2 RNAs is irrelevant to regulation of the sexual phenotype, which seems unlikely, or there is additional complexity within the hierarchy of sex determining genes, such as feedback regulation, which ensures that the tra-2 product corresponds to phenotypic sex.