B cells develop in the mammalian bone marrow through a sequence of precursor stages, which can be ordered by the recombination status of their immunoglobulin loci. This developmental pathway is functionally similar between mice and man. However, whether this similarity is based on usage of the same genes is unknown. We show that large-scale gene expression patterns differ substantially between human and mouse B-cell development. Among 644 genes which were differentially expressed in 4 early stages of human B-cell development, only 48, 86, and 75 genes could be identified, which are upregulated in both human and mouse pre-BI, large pre-BII, and small pre-BII cells, respectively. A comparison of mouse B- and T-cell development reveals that gene expression patterns of early murine B- and T-cell precursors are most similar, whereas in more differentiated precursors, human and mouse B cells have a more similar gene expression profile. We conclude that large-scale differences in gene expression patterns between human and mouse B-cell precursors may stem from either selective neutrality or compensatory evolution, whereas the few similarities may stem from negative selection. Gene expression patterns are shaped by ontogenic relationships in early and by functional specialization in later stages of development.