To detect the t(11;18) chromosome translocation in different stages of mucosa-associated lymphoid tissue (MALT) lymphoma, we established a RT-PCR method by adopting three new primer pairs and using the RNA extracted from the paraffin tissues to amplify the t(11;18) fusion gene API2-MALT1 in shorter lengths. Our results showed five key findings, which are (a) higher detection rates of t(11;18) (21.13%) in Chinese patients with transformed MALT lymphoma, (b) lower detection rates of t(11;18) in stomach MALT lymphoma, (c) different organ localizations of MALT lymphoma in Chinese patients, (d) higher nuclear expression rates of Bcl-10 in low grade MALT (51.72%), and (e) lower response rates (50% CR, and 50% PR) to anti-H.-pylori therapy. These findings suggest novel pathways for low-grade MALT lymphoma to be progressed into transformed MALT lymphoma. This study also suggests that amplification of shorter length of PCR products from the paraffin-fixed tissues increases sensitivity, which is significant in improving the selection of the therapeutic regimen and assessing the prognosis of the disease.