Gastrointestinal stromal tumors (GIST) are rare neoplasms of unknown etiology and pathogenesis. Their clinical behavior is very unpredictable and a reliable prognostic factor is lacking. The aim of this study was to analyze some prognostic factors and estimate which one is the most reliable. Thirty-eight biopsy specimens of GIST were immunolabeled for PCNA, CD34, vimentin, NSE and actin. The greatest diameter, histological grading, mitotic count, DNA-index and S-phase were estimated for each case. All patients were followed-up for at least 24 months or to death. The data were analysed by univariate and multivariate statistical analysis using a computer program. The results showed that greatest diameter, tumor grade, mitotic count and PCNA-index are prognostic factors in univariate analysis. In multivariate analysis only the greatest diameter is a useful prognostic factor for planning further therapy.