The gene for the T-cell antigen receptor (TCR) delta chain is a gene within a gene, being located in the TCR alpha chain gene in both mice and humans. The human delta locus is flanked by delta deleting elements that undergo preferential rearrangement in the thymus, resulting in deletion of internal delta coding segments. The mouse has conserved analogous elements, m delta Rec and m phi J alpha, which separate delta from alpha and undergo a m delta Rec/m phi J alpha rearrangement in polyclonal thymus. The 5' element, m delta Rec, which is an isolated heptamer-spacer-nonamer (h-s-n), lies within 200 kb of D delta 1, and displays two areas of nearly 80% homology to human delta Rec. The downstream element, m phi J alpha, lies 12.5 kb 3' to C delta, lacks the consensus amino acids for J alpha, and retains 80% homology to human phi J alpha. Cells from murine neonatal thymus show three prominent m delta Rec rearrangements consisting of the m delta Rec/m phi J alpha recombination, a delta Rec/D delta 1/D delta 2/J delta 1 recombination, and two hybrid recombinations. A consequence of the m delta Rec/M phi J alpha rearrangement is a deletion of internal D delta and J delta coding segments that would prevent their incorporation into alpha TCR products. The conservation of noncoding deleting elements flanking the delta TCR in mice and humans is similar to the evolutionarily preserved kappa deleting element of the B-cell lineage and argues for an important role in receptor utilization.