The applicability of T cell receptor (TCR) Ddelta2Ddelta3 junctional regions for the detection of minimal residual disease (MRD) was examined in childhood acute lymphoblastic leukemia (ALL). Southern blot analysis showed a Ddelta2Ddelta3 rearrangement in 22 of 172 (13%) precursor-B ALL. No Ddelta2Ddelta3 rearrangement was identified in 29 T-ALL cases. Three patients exhibited Ddelta2Ddelta3 recombinations in both alleles. Sequence analysis of Ddelta2Ddelta3 junctions revealed extensive diversity due to the random insertion and deletion of nucleotides at the joining site. PCR analysis utilizing allele-specific probes or oligonucleotides generated on the basis of Ddelta2Ddelta3 junctional sequences reached a sufficient sensitivity of 10(-4) to 10(-5) in the majority of cases. In four of 25 (16%) rearranged alleles, however, the 5' heptamer-nonamer recombination signal sequence (RSS) of the Ddelta2 segment had recombined directly to the 3' heptamer-nonamer RSS of the Ddelta3 segment thus generating a so-called signal junction. Respective heptamer-heptamer junctions are not suited to design allele-specific oligonucleotides for the detection of MRD because of their limited diversity and hence specificity.