Differential diagnosis of Burkitt lymphoma (BL), diffuse large B-cell lymphoma (DLBCL) and B cell lymphoma, unclassifiable, with features intermediate between BL and DLBCL (intermediate BL/DLBCL) can be difficult. We studied 97 Chinese pediatric mature aggressive B-cell lymphomas including 81 BL cases, eight DLBCL cases and eight intermediate BL/DLBCL cases using immunohistochemistry, interphase fluorescence in situ hybridization (FISH) and Epstein-Barr virus (EBV) in situ hybridization. Our results showed that there were no significant differences in the expression of CD10 and BCL6 among cases of BL (91% and 86%, respectively), DLBCL (75% and 63%, respectively) and intermediate BL/DLBCL (75% and 63%, respectively) (p > 0.05). The expression of BCL2 (3% in BL, 50% in DLBCL, 50% in intermediate BL/DLBCL), expression of MUM1 (17% in BL, 63% in DLBCL, 63% in intermediate BL/DLBCL) and mean Ki-67 proliferation index (PI) (93% in BL, 83% in DLBCL, 80% in intermediate BL/DLBCL) were significantly different between BL and DLBCL and between BL and intermediate BL/DLBCL. The frequency of an extra copy of BCL6 (0% in BL, 37.5% in DLBCL, 25% in intermediate BL/DLBCL) and EBV-encoded RNA (EBER) positivity (48% in BL, 0% in DLBCL and intermediate BL/DLBCL) were also significantly different between BL and DLBCL and between BL and intermediate BL/DLBCL. The frequency of C-MYC rearrangement in BL (98%) was much higher than in DLBCL (37.5%) and intermediate BL/DLBCL (50%). Our findings suggest that diagnosis of the mature aggressive B-cell lymphomas in pediatrics should be based on the comprehensive review and integration of morphological, immunohistochemical and molecular genetic features. The expression of CD10 and BCL6 but not BCL2, a high Ki-67 PI (>90%) and a C-MYC rearrangement but not BCL2 or BCL6 rearrangement are the features of BL. MUM1 is not an exclusionary diagnostic marker for BL. As the immunophenotype and molecular genetic features of DLBCL and intermediate BL/DLBCL are similar, intermediate BL/DLBCL is more likely a subgroup of DLBCL in the pediatric population. Regardless of the expression of CD10 and BCL6, strong staining for BCL2, Ki-67 PI below 90% and the presence of extra copies of BCL6 favor a diagnosis of DLBCL or intermediate BL/DLBCL.