Diagnosis of gastric malignant lymphoma remains a challenge, especially when the tissue source is endoscopic biopsy specimens. Once an atypical lymphoid infiltrate is found, demonstration of clonality is the key to establishing a diagnosis of the disease. For this purpose, we evaluated the usefulness of immunohistochemistry, in situ hybridization, and polymerase chain reaction (PCR) using formalin-fixed, paraffin-embedded endoscopic materials from 20 patients with B-cell malignant lymphomas. Template DNA for PCR was obtained by microdissecting Giemsa-stained sections using a serial hematoxylin and eosin section as a guide. Clonal rearrangement bands were demonstrated in 15 of 20 cases (75%) by PCR, whereas expression of monotypic light-chain mRNA was detected in seven of 20 (35%) by in situ hybridization and monotypic light-chain restriction in four of 20 (20%) by conventional immunohistochemistry. Although less sensitive than PCR, in situ hybridization was useful for localizing the expression of target mRNAs with cellular accuracy and with low background staining. In addition, two cases were found to be monoclonal only by in situ hybridization, and not by PCR. The results showed that clonal proliferation is detected with the greatest sensitivity with PCR using small routinely processed biopsy specimens and that a difficulty with the PCR method in terms of cellular localization was partially overcome using a microdissection procedure that provided at least tissue-level accuracy.