We performed loss of heterozygosity (LOH) analysis on matched lymph nodes before and after progression of follicular lymphoma (FL), and found novel LOH on chromosome arm 12p. This LOH has not been previously reported in association with FL transformation. Other sites of frequent LOH include chromosome arms 6q and 9p. LOH was observed in both transformed FL and relapse FL. These data suggest that altered tumor suppressor genes exist on 6q, 9p, and 12p that have an important role in the progression of FL. Genetic changes accumulated in relapsed FL in the absence of histological changes compared to initial diagnosis.