The T cell receptors (TCR) in HLA-B27 (B*2705) alloreactivity were analyzed in cytotoxic T lymphocytes (CTL) from two individuals. Non-random usage was found in V beta, N+D beta, V alpha, and J alpha, but not in J beta segments or N alpha-regions. V beta segments from homology subgroup 4 were predominant and not associated to a particular donor or fine specificity, suggesting involvement in recognizing the HLA-B27 molecule. In contrast, preferential V alpha usage was associated with particular individuals and fine specificities, indicating distinct V beta and V alpha recruitment and contribution to allorecognition. Recurrent N+D beta motifs and J alpha segments, even from different donors, limited junctional diversity, suggesting that CDR3 usage was determined by the alloantigenic epitope independently of individuals. TCR were selected differently at various levels, as indicated by the following findings. Four clonotypes with similar fine specificity had identical beta and unrelated alpha chains. Similar alpha were associated with unrelated beta chains, and vice versa. CTL using V beta subgroup 4 did not globally show concomitant predominance of other TCR elements. V alpha 7, one of the preferred V alpha segments, was always associated with V beta subgroups other than 4. Sometimes, a TCR showed homology in elements of one chain to a second TCR or group of TCR, and to another in the other chain. These results are best explained by differential selection of TCR elements by different epitopes, providing a key to the inner structure of allospecific TCR repertoires.