We have investigated the structure of the Ig heavy (IGH) chain locus in 309 cases of acute leukemia. Seventy-one cases of B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) were analyzed: in six cases deletion of joining (JH) segments in the presence of cytogenetically normal chromosome 14 was observed. Similar deletions were seen in 1 out of 8 cases of biphenotypic acute leukemia analyzed: this case exhibited t(9:22)(q34;q11) and coexpressed both myeloid and B cell differentiation antigens. Five of the 7 cases analyzed had deleted the JH segments from both chromosomes. Because these deletions may have contributed to the pathogenesis of the disease we have attempted to define their boundaries. Using probes that map both 5' and 3' of JH, the 3' (centromeric) boundary of the deletions was mapped to an approximately 30-kb central region of the 60 kb between C delta and C gamma 3 in 10 of the 12 deleted chromosomes. In the remaining two chromosomes, the 3' boundary mapped to S mu. The 5' (telomeric) boundary could not be defined. However, three cases with biallelic deletion of JH showed biallelic deletion of the most proximal variable (VH) (VH6 and VH5-B2) genes, indicating that the deletions spanned over 500 kb. VH5-B1 and VH5-B3 were retained in germline configuration and no gross deletions were observed using a VH3 subgroup-specific probe, indicating that the 5' boundary mapped within the VH locus. Unusual deletions of the portion of the IgH locus including JH segments and the C mu and C delta genes may occur in acute leukemias with immunophenotypic evidence of commitment to the B cell differentiation pathway. The possible consequences of the deletions remain to be determined. However, the clustering of the centromeric boundary of the deletions to S mu and to a region between the C delta-C gamma 3 genes, a known "hot spot" for recombination, may indicate the operation of a distinct pathogenic mechanism.