Recent reports show an increase in the rate of lymphoid malignancy among children. Previous studies also indicate that approximately 50% of all lymphoid malignancies contain rearrangements between antigen receptor genes and oncogenes, suggesting that V(D)J recombinase fidelity may be involved in the development of these malignancies. Although normally V(D)J recombinase assembles functional antibody and T cell receptor genes from numerous noncontiguous variable, diversity, and joining segments within one locus, it can occasionally rearrange DNA segments from two distinct loci (trans-rearrangements). In order to examine the fidelity of V(D)J recombination, we have modified a PCR-based assay (Lista, et. al. Cancer Res. 57:4408,1997) to improve the quantitation of aberrant events occurring between two T cell receptor loci (TCRγV-TCRβJ) in the thymus cell population of mice. Reconstruction experiments to evaluate the assay's sensitivity revealed the ability to detect a single trans-rearrangement in 1µg of DNA (1.5 x 10 5 thymocytes). Trans-rearrangement frequencies were estimated by analyzing multiple PCRs from individual mice. The baseline transrearrangement frequencies per cell for Balb/c, C57BL/6, B6C3F1, and AKR mouse strains were 4.3 x 10 -6 , 5.0 x 10 -6 , 6.1 x 10 -6 , and 2.5 x 10 -6 , respectively. DNA sequence analysis of the rearrangements revealed hallmarks of V(D)J mediated recombination, including consensus sequence cleavage, end nucleotide nibbling, and non-template derived nucleotide addition. With this new assay we will be able to evaluate various environmental and occupational exposures during various lifestages for their effect on this important mechanism of carcinogenesis.