The effect of thymic selection on the expressed human T-cell antigen receptor beta-chain variable region (V beta) gene repertoire was examined by using a multiprobe RNase protection assay. The relative abundance of transcripts for 22 V beta genes (encompassing 17 of the 20 human V beta gene subfamilies) within a thymus, and among 17 thymuses, was variable. On the basis of the presence of corresponding mRNAs, no genomic deletions were detected, but several coding region polymorphisms were identified. Analysis of mature T-cell subsets revealed the absence of complete "superantigen"-mediated V beta deletions, suggesting that this phenomenon, in contrast to mouse, is uncommon or absent in humans. However, several V beta genes were over- or underexpressed in one or both mature single-positive (CD4+8- or CD8+4-) thymocyte subsets compared to syngeneic total, mostly immature thymocytes. Whether these changes are induced by relatively weak superantigens or conventional antigens and whether the downshifts are caused by negative selection or lack of positive selection remains to be determined.