The levels of protooncogene RNA in matched bone marrow and peripheral blood cells obtained from patients with newly diagnosed acute myelogenous leukemia were compared. While the absolute amounts of c-myc RNA in the matched specimens are similar, the levels are not correlated. In contrast, while the levels of c-fos RNA in the matched bone marrow and peripheral blood cells are correlated, the absolute levels of c-fos RNA differ substantially. The level of histone H3 RNA is higher in bone marrow cells than in peripheral blood cells. These substantial differences in protooncogene RNA levels between leukemic cells found in the bone marrow and in the peripheral blood make it impossible to accurately "characterize" gene expression in leukemic cells if studies are restricted to the cells in either compartment. Additionally, there appears to be a significant relationship between the levels of c-fos RNA and triose phosphate isomerase RNA and the height of the white blood cell count and between the level of c-fos RNA in marrow cells and the proportion of monocytic cells present.