It is often difficult to differentiate extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma) from non-neoplastic inflammatory conditions. Demonstration of clonal lymphoid proliferation by molecular procedures is important for accurate diagnosis. We examined the clonal population of B-cell lymphomas in nine cases of thyroid and two cases of salivary gland B-cell lymphoma using semi-nested polymerase chain reaction (PCR)-based assay for IgH gene arrangement and reverse transcription (RT)-PCR single-strand conformation polymorphism (SSCP) for the detection of IgL gene rearrangement. Clonality was evident in nine out of 11 cases of B-cell lymphomas examined by PCR, and in six of eight cases by RT-PCR SSCP. In addition, analysis of VH families was performed in eight cases. Although VH3 family was frequently used, each case demonstrated the VH4, VH5 or VH6 family. It is possible that the normal counterpart of thyroid or salivary gland lymphoma might be different from peripheral blood B lymphocytes, which usually use VH3 family. Our results indicate that although no clonality was noted in one case by both PCR and SSCP, these molecular methods are useful as supplementary diagnostic tests for both thyroid and salivary gland lymphomas.