Distinguishing between thyroid malignant lymphoma and lymphocytic thyroiditis (Hashimoto's thyroiditis) is quite difficult and problematic. B cell lymphomas display clonal Ig heavy-chain (IgH) gene rearrangement, and Southern blot hybridization (SBH) is often used for detection of the monoclonality of the IgH gene. However, SBH is often problematic because it requires a large volume of samples. We examined the efficiency in detecting the monoclonality of IgH gene in thyroid malignant lymphomas by vectorette PCR, which we started with only 200 ng of genomic DNA. Monoclonality was detected in 36 of 47 (76.6%) malignant lymphomas, whereas it was not detected in 10 samples of tissue of Hashimoto's thyroiditis. The sensitivity was almost the same as that with SBH in which monoclonality was detected in 33 of 45 (73.3%) malignant lymphomas. These results suggest that vectorette PCR may be a substitute for SBH, and because it requires only a small volume of samples, it may be used in the analysis of aspiration biopsies.