Abstract: Objective : To investigate the expression of various variants of API2- MALT1 fusion gene in MALT lymphoma and its effects on the clinicopathological feature and prognosis of MALT lymphoma. Methods : Twenty-nine archival cases of gastric and pulmonary MALT lymphoma were selected and reviewed. Five cases of chronic lymphoadenitis were used as negative control. Four kinds of variant of API2-MALT1 fusion gene and β-actin mRNA (internal control) were assayed in all samples by RT-PCR and nested PCR. Twenty-nine samples were divided into two groups in terms of the expression of API2-MALT1 mRNA or not. The relationship between the expression and the clinicopatho-logical feature and prognosis of MALT lymphoma was investigated by the stains of HE, IHC and followup. Results : β-actin was detected in all samples. Two variants of the fusion gene were found in 14 of 29(48.2%) cases with MALT lymphoma(gastric MALT lymphoma : 9/19, 1446/1123 predominantly; pulmonary MALT lymphoma: 5/10, 1446/814, predominantly), and none of chronic lymphoadenitis. Comparing with those without API2-MALT1 mRNA,the staging(P=0.134), cellular proliferation(P=0.0870)and involvement of lymph node (P=0.0541) tended to be lower and milder in the group with API2-MALT1 fusion transcript, there were no distinct difference in the extent of lesion, the depth of invading and prognosis between two groups. Conclusion : The expression of API2-MALT1 mRNA may be associated to the staging, involvement of lymph node and cellular proliferation of MALToma, but not to the extent of lesion, depth of invading and prognosis of MALToma. The expression of the different variants mare correlated with the site of MALT lymphoma.