Flow cytometric immunophenotyping (FCI) is recognized as a rapid, sensitive, and accurate method for diagnosis of B-cell lymphomas. We observed that FCI failed to identify the clonal B-cell population in several cases of large B-cell lymphoma (DLBCL) when tissue samples were prepared by a commercially available mechanical tissue disaggregation method. We tested a manual tissue disaggregation method and compared it with the mechanical method. FCI findings from 51 cases of DLBCL processed with the mechanical tissue disaggregation method, 27 cases processed using the manual method, and 15 cases processed using a combination of both methods were compared. The histological and immunohistochemical findings in each case were reviewed. FCI detected a clonal B-cell population in 88.9% of cases processed by the manual tissue disaggregation method, 66.7% of cases processed by a combination of the manual and mechanical disaggregation methods, and in 62.7% of cases processed solely by the mechanical tissue disaggregation method (P < 0.01 Fisher exact). Manual processing yielded positive FCI results in 81.8% of the nodal tissue samples and 93.8% of the extra-nodal tissue samples, whereas mechanical disaggregation was particularly inefficient in preserving large lymphoma cells from extra-nodal tissue: 71.4% of the nodal and 56.8% of the extra-nodal tissue samples processed by the mechanical method showed clonal B-cells by flow cytometry (P < 0.006, Fisher exact). The diagnostic yield of FCI in DLBCL can be significantly improved by utilizing a manual disaggregation method, particularly in extra-nodal tissue samples. © 2015 International Clinical Cytometry Society.