Given that the studies on human small intestinal stromal tumors are very limited, our study was designed to determine the significance of apoptosis, the role of some apoptosis-related proteins, including Bax, Bad, Bid, Bcl-2, Bcl-Xl, and Bcl-W, in jejunal stromal tumors (JST). For this purpose, 52 samples were examined by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling and immunohistochemistry, including 40 cases from normal jejunum and 12 cases from the JST. The results showed that a significantly decreased apoptosis was observed in JST compared with normal jejunum (median of apoptotic index, 0.13% vs 15.17%, p < 0.001). In univariate analysis, statistically significant differences were shown in percentage of positive-expression of Bid (0.0% vs 77.5%, p < 0.001), Bcl-2 (91.7% vs 42.5%, p = 0.003), and Bcl-Xl (75.0% vs 35.0%, p = 0.014), but not in Bax, Bad, and Bcl-W. Moreover, Bcl-Xl was an independent parameter associated with JST by multivariate Logistic analysis. For the role of ratios of anti-apoptotic proteins to pro-apoptotic proteins, Bcl-Xl / Bid ratio was the most preferable index. In conclusion, decreased apoptosis and expression of Bid, increased level of Bcl-Xl may play some important roles in human JST, and Bcl-Xl / Bid ratio may be as a new potentially associated index, although they should be validated in more studies.