Gastrointestinal stromal tumors (GISTs) are a heterogenous group of mesenchymal neoplasms ranging from semibenign tumors to highly aggressive neoplasms. Predicting their clinical behavior is challenging and criteria delineating benign from malignant cases are controversially discussed. The aims of the present study were to define the clinicopathological features of 35 GISTs and to determine whether any specific parameters were associated with the patient's outcome. In the present series, protein S100 (S100) expression was found in 13/35 (37%) patients with a varying staining intensity ranging between strong and moderate. The multivariate statistical analysis in the S100-positive group revealed a significantly poorer survival (p = .0058) and a tendency for higher recurrence (p = .052) compared to the negative GIST patients. Furthermore, the statistical analysis disclosed a correlation between the expression of CD117, CD34, desmin, and alpha-smooth muscle actin and survival or recurrence (p > .05). Positive immunoreactivity was seen for CD117 in 25 (71%) patients and for CD34 in 19 (54%) patients. In addition we confirmed the previously reported impact of initial tumor size on survival and recurrence rate (p = .034 and p = .039). The series was also analyzed according to established prognostic factors (tumor size and mitotic activity), which indicated that 77% of S100-positive cases were at high risk for malignant tumor behavior, 15% at intermediate risk, and 8% at low risk. Based on these findings, we suggest that protein S100 represents an additional prognostic factor to better define the malignant potential of GISTs and stratify the risk for each patient.