JL1 is a novel molecule expressed in the surface of hematopoietic precursor cells, but not on any other mature human tissue. Accordingly, JL1 is expressed in acute lymphoblastic leukemia (ALL) cells and can be used both for specific diagnosis and as a target for treatment. However, expression of JL1 by lymphomas has not been thoroughly assessed. Burkitt lymphoma is a potentially curable aggressive lymphoma, but prognostic markers that stratify risk have not been established. We therefore assayed JL1 expression in Burkitt lymphoma patients to assess its value as a prognostic marker for this disease. Tissue microarray blocks of formalin-fixed paraffin-embedded tissue samples from patients with Burkitt lymphoma and other B-cell lymphomas, at the Asan Medical Center and Seoul National University Hospital from January 1998 to December 2008 were immunohistochemically assayed using a mouse monoclonal antibody against JL1. We found that 30.2% of Burkitt lymphoma samples, but no other lymphoma samples, were positive for JL1. JL-1 expression was significantly correlated with patient survival (P = 0.022), but not with other clinical manifestations of the disease, with 91.6% of JL1-positive patients achieving complete remission in response to chemotherapy and 6.25% experiencing disease recurrence. JL1 positivity was significantly correlated with prolonged overall survival by both Kaplan-Meier survival (P = 0.035) and Cox proportional hazard model (P = 0.043) analysis. JL1 expression in Burkitt lymphoma was positively correlated with overall survival and better response to chemotherapy, suggesting that JL1 may be a prognostic marker for risk stratification in these patients.