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The diagnostic impact of bone marrow cytology in combination with flow cytometry analysis of aspirate smears and bone marrow histology together with immunohistochemical examination of trephine biopsies was compared in 141 routine cases. Diagnoses achieved by the two methods were concordant in 80.5% of cases. In discordant cases, clinical follow-up data of at least one year confirmed the correctness of cytological and histological diagnoses. For infiltration by malignant disease, both methods were concordant in 86.5% of samples and correlated well for the degree of infiltration (r = 0.64, p <0.001). Overall, regression analysis showed a good correlation for cellularity (r = 0.67) lymphopoiesis (r = 0.75), granulopoiesis (r = 0.73) and megakaryopoiesis (r = 0.65) while erythropoiesis displayed a lower degree of correlation (r = 0.43, all p <0.001). Regression analysis on all immunological data obtained by flow cytometry (FC) and immunohistochemistry (IHC) showed a good overall linear correlation (r = 0.67, p <0.001), but significant differences were found for a few phenotypic markers. Furthermore, the correlation was found to be dependent on IgG subclasses and the fluorochromes used for FC. Thus, analyses with IgG2 antibodies and phycoerythrin (PE) as fluorochrome showed significantly more expression than IHC. In conclusion, cytology and histology, both in association with the respective immunophenotyping, are of equal value in bone marrow diagnostics and should be used in combination. However, in some specific settings, one of the two procedures might be preferable.