An abnormal expression of cyclin D3, a key regulator of the cell cycle, has been documented in a variety of human malignancies, and the cyclin D3 gene, mapping to 6p21, may be deregulated in human tumors as a result of the t(6;14)(p21.1;q32.3) translocation or gene amplification. In the current study, we for the first time investigated by immunohistochemistry and fluorescence in situ hybridization (FISH) the prevalence of cyclin D3 abnormalities in gastrointestinal stromal tumors (GISTs), comparing the results with traditional pathological characteristics, p27 immunoreactivity (IR), and Ki-67 labeling index (LI). All the tumors showed nuclear cyclin D3 IR, with a percentage of immunostained neoplastic cells ranging from 10 to 95% (mean, 67.3 +/- 22.9%). In 4 (40%) of the 10 cases analyzed by FISH, cyclin D3 extrasignals were detected. Cohybridization with probes specific for the centromeric region and the long arm of chromosome 6 indicated trisomy in one case, whereas in the remaining three cases the pattern was highly suggestive for the occurrence of an isochromosome 6p. There was no association between the cyclin D3 gene copy number and IR for the encoded protein. Cyclin D3 IR was positively associated with p27 IR (P =.004) but not with Ki-67 LI or tumor malignant potential. On the contrary, p27 IR was inversely associated with Ki-67 LI (P =.004) and was more prevalent in tumors of low or intermediate malignant potential, though at a borderline level of statistical significance (P =.066) only. These data suggest that cyclin D3 expression in GISTs is independent of gene amplification and that this protein may be involved in the pathogenesis of GISTs by counteracting the inhibitory activities of p27.