The prognosis of salivary gland adenoid cystic carcinoma (ACC) depends on the clinical stage, the location of the primary tumor, and the histologic growth pattern. ACCs with a cribriform growth pattern have a better prognosis than those with a solid growth pattern; however, clear-cut grading criteria have not yet been established, and therefore prognostic indicators on a molecular level are of special interest. In order to analyze tumor tissue with different growth patterns, cribriform and solid tumor areas of 25 patients were microdissected and separately analyzed for loss of heterozygosity (LOH) at nine polymorphic microsatellite markers located between 6q14 and 6q27. LOH was detected in 19/25 (76%) patients and LOH rates were highest at markers D6S441, D6S310, D6S311 and UTRN, which are located at 6q23-25. Combined analysis of LOH at these four markers shows that in primary tumor subtype foci with cribriform growth pattern LOH is associated with high TNM stages (P<0.01), high T stages (P=0.01), positive lymph node status (P=0.03), an unfavorable disease course (P=0.02), and the presence of >10% solid growth pattern (P=0.05). In contrast, in primary tumor subtype foci with solid growth pattern, no significant differences in LOH rates were found in patients from prognostically and histologically favorable versus unfavorable patient groups. The frequent occurrence of LOH at 6q23-25 and the correlation of LOH rates with prognostic parameters indicate that a prognostically important tumor suppressor gene is located in this chromosomal area.