Deletion of chromosome 6q has frequently been observed in natural killer (NK) cell lymphomas. The aim of this study, is to localize the commonly affected region in chromosome 6q and to compare the frequency of loss of heterozygosity (LOH) between the peripheral T and NK cell lymphomas. Eight cases of peripheral T cell lymphomas, not otherwise characterized (PTCL-NOC), and 5 cases of nasal-type NK/T cell lymphomas were enrolled for the study. Twelve polymorphic markers covering the regions from 6q13 to 6q24, according to the Entrez Database (National Center for Biotechnology Information, NIH, Bethesta, MD), were used for LOH analysis. Results showed LOH at least one locus on chromosome 6q was observed in all cases. Of the informative cases, the overall frequency of LOH for each marker ranged from 8.3 to 58.3%. NK/T cell lymphomas showed a higher frequency of LOH compared to the PTCL (47.44 +/- 12.39 vs. 30.89 +/- 11.97%). The average frequency of LOH was 31.93 +/- 16.04% in stages I + II of the disease, whereas the average was 45.78 +/- 4.15% in stages III + IV. The most frequently involved regions were at markers D6S434 (5 of 8 informative cases, 62.5%) on chromosome 6q16.3 in the PTCL, D6S302 (4 of 5 cases, 80%) on chromosome 6q21 and D6S287 on 6q22.3 (4 of 5 cases, 80%) in the NK/T cell lymphoma. In conclusion, LOH of chromosome 6q is more common in nasal-type NK/T cell lymphoma than PTCL. The difference between the commonly lost region of chromosome 6q in NK/T cell lymphoma and that in PTCL suggests that different tumor suppressor genes are involved in the genetic evolution pathway of these two diseases.