The aim of this study was to test and establish the accuracy and reliability of lymphoma classification in bone marrow trephines according to the new World Health Organization (WHO) classification by considering predominantly the morphology and immunophenotype. Therefore, we retrospectively compared lymphoma diagnoses, rendered exclusively on bone marrow trephines without knowledge of lymph node diagnosis in 124 patients, with the results of the reference centres that had reviewed lymph node (n = 90) or extranodal biopsies (n = 34). The overall concordance rate was higher than 85% and 91%, respectively, when patients with discordant malignancy grades were excluded. The concordance rate for low-grade B-cell lymphomas was 93% and for high-grade B-cell lymphomas 84%. The main reasons for discordant diagnoses were divergent immunophenotypes among low-grade B-cell lymphomas (6 out of 81, i.e. 7.4%) and discrepant malignancy grades within high-grade B-cell lymphomas (6 out of 31, i.e. 19.4%). No relationship between discordant diagnoses and chemotherapy given during the course of the disease with the site of biopsy (i.e. lymph nodes, extranodal sites) was noted. We conclude from our results that bone marrow trephines are a reliable tool, not only for establishing bone marrow infiltration, but also for the subtyping of lymphomas.