Objective To evaluate the usefulness of in situ hybridization for Immunoglobulin κ and λ light chain mRNA to detect light chain restriction in the diagnosis of primary gastric lymphoma (PGL) of mucosa-associated lymphoid tissue (MALT) type. Methods Twenty-seven cases of PGL of MALT type and 5 cases of gastritis were analyzed using in situ hybridization with fluorescent isothiocyanate (FITC)-labeled oligonucleotide probes for κ and λ light chain mRNA. The κ∶λ ratios of tumor cells,lymphocytes and plasma cells were analyzed to detect light chain restriction and clonal plasma cells. Results Light chain restriction was found in 10 of 27 (37%) cases of PGL cases (in 5/9 low grade and 5/18 in high grade). Clonal plasma cells were detected in low grade but not in high-grade cases. No light chain restriction was found in gastritis specimens, the adjacent tissue of tumors or the distant stomach mucosa in lymphoma cases. Conclusions The detection of clonality using mRNA in situ hybridization could be a helpful diagnostic tool for gastric lymphoma. The presence of clonal plasma cells can be a marker of the early lesion of low-grade PGL.