OBJECTIVE: To compare and evaluate the sensitivity, specificity, and prognostic value of various assays for bone marrow involvement in patients with non-Hodgkin's lymphoma (NHL). METHODS: A total of 351 patients with NHL who underwent concurrent bone marrow biopsy in Third Hospital of Peking University from January 2013 to November 2017 were selected. Bone marrow biopsy (BMB), flow cytometry (FCM), gene rearrangement detection, and bone marrow morphology examination were performed for evaluation of bone marrow involvement. Bone marrow biopsy was used as the gold standard, the sensitivity and specificity of FCM, gene rearrangement and bone marrow morphology of bone marrow aspirate were analyzed, and their ROC curves were drawn. In the survival analysis of 77 patients with NHL, the overall survival (OS) time, progression-free survival (PFS) time, and complete remission rate (CRR) were counted. The survival of patients in the FCM positive group, the gene rearrangement positive group, the positive control group (BMB positive group) and the negative control group were compared. RESULTS: The detection rate of flow cytometry and gene rearrangement of bone marrow aspirate both were higher than that of bone marrow biopsy and bone marrow morphological examination, showing better diagnostic efficacy. The sensitivity of the combined method of flow cytometry and gene rearrangement was 82.5%, while the specificity was 90% and the AUC was 0.863. The gene rearrangement detection of bone marrow aspirate possessed the role suggesting the poor prognosis for NHL patients. The 3-year survival rate of patients in the gene rearrangement-positive group (RG group) was lower than that of patients in the no-bone involvement group (All negative group) (P＜0.05). Although the survival curve of patient in RG group was not significantly different from that of patients in All negative group (P＜0.1), it still showed a poor prognosis for NHL patients. And the significance of predicting death risk was reflected in Cox regression model (P＜0.05). There was no statistical difference in the prognosis of patients in the FCM-positive group (FCM group). CONCLUSION: In the bone marrow aspirate tests, flow cytometry and gene rearrangement detection have good diagnostic efficiency, and gene rearrangement can suggest the prognosis of patients. The combined detection efficacy of two methods is better.