The tumor protein D52 gene or protein is frequently overexpressed in several carcinomas, and has been identified as a B cell differentiation marker. D52-like genes are also differentially expressed in particular haematological malignancies, where transcript or protein levels may reflect cellular proliferative or differentiative status. We used RT-PCR to analyse the expression of three D52-like genes in bone marrow at the time of ALL or AML diagnosis in children. Whereas D53 transcripts were undetectable in all samples, D52 and D54 transcripts were frequently detected in ALL and AML, where they were frequently co-expressed. While D52 and D54 transcripts were detected in T-ALL and pre-B ALL at comparable frequencies, D52 was less frequently detected in ALL bone marrow with hyperdiploid karyotypes, compared with samples with normal karyotypes. We also found that total RNA yields significantly differed according to D52 and D54 expression status, and that bone marrow freezer storage time (up to 945 days) differed significantly according to D52 expression status. These results indicate that D52-like genes are not ubiquitously expressed in leukemic bone marrow in children, and that RNA sample parameters may influence measures of gene expression more than commonly appreciated.