Enumeration of total nucleated cells and mononuclear cells is a fundamental part of the laboratory evaluation and quality control program for bone marrow and peripheral blood stem cell collections intended for transplantation. Measurement of the total nucleated cell content is especially useful for providing rapid feedback about the bone marrow product during or immediately after the harvest. However, the mononuclear cell content may be more informative because the nucleated cell population contains a variable number of mature granulocytes and nucleated red cells, which do not contribute to hematopoietic engraftment. The lack of comparative data among various laboratories and among different types of cell counting methods has hindered standardization of these assays among bone marrow processing laboratories. Specific issues needing attention in assay standardization include sample preparation and handling, identification and elimination of artifacts in automated counting, relative advantages and disadvantages of manual and automated counting methods, and criteria for differential counting of nucleated cells. The establishment of standards for bone marrow and other stem cell counting methods, as well as other evaluation procedures, should be preceded by collection and analysis of comparative data, and followed by a proficiency testing program for bone marrow processing laboratories.