To analyze the association of several types of malignant lymphomas in different anatomical sites with the Epstein-Barr virus (EBV) infection status, 127 cases of formalin-fixed paraffin-embedded samples of malignant lymphomas were investigated with in situ hybridization detecting EBV-encoded small RNA (EBER) in tumor cells. Forty-six out of 108 non-Hodgkin lymphoma (NHL) cases were positive for EBER (42.6%). The EBER-positivity rate of NHL in the nasal cavity and nasopharynx (35/60 cases, 58.3%) was higher than that of NHL in stomach (9/30 cases, 30%) and in the superficial lymph nodes (2/18 cases, 11.1%) (P<0.05). The EBER-positivity rate of Hodgkin lymphoma in the superficial lymph nodes was 26.3% (5/19 cases). These findings suggest that the EBV-positivity rate in lymphomas is related to their histological types and locations.