Pathomorphological examination of trephine biopsies of the bone marrow (BM) represents a standard method for the diagnosis and staging of hematologic neoplasms and other disorders involving the BM. The increasing knowledge about the genetic basis and biology of hematologic neoplasms, as well as the recently proposed WHO classification system, provide the framework for an accurate diagnosis. Although conventional morphology remains the gold standard for paraffin-embedded BM trephines, immunohistochemical stainings have become an integral part of the diagnostic workup. Antibodies suitable for paraffin sections are generally applicable to BM trephines, but modifications of staining protocols may be necessary due to the alternative fixatives and decalcification procedures used for BM biopsies. The indications for immunostainings range from confirmation and classification of lymphoma involvement, subclassification of acute leukemias, and estimating blast counts in myelodysplastic and myeloproliferative syndromes to characterization of BM involvement in nonhematologic neoplasms. Although subtyping of NHL in the BM is more difficult from the point of morphology, classification of the entities that frequently involve the BM, especially the small B-cell lymphomas, can easily be achieved with the help of immunohistochemistry. In this review, we try to summarize the current state of the art in BM immunohistochemistry for the diagnosis of hematologic disorders. Moreover, diagnostic algorithms and useful antibody panels are proposed for a rational and cost-effective approach.