As a new method, support vector machine (SVM) were applied for prediction of toxicity of different data sets compared with other two common methods, multiple linear regression (MLR) and RBFNN. Quantitative structure-activity relationships (QSAR) models based on calculated molecular descriptors have been clearly established. Among them, SVM model gave the highest q2 and correlation coefficient R. It indicates that the SVM performed better generalization ability than the MLR and RBFNN methods, especially in the test set and the whole data set. This eventually leads to better generalization than neural networks, which implement the empirical risk minimization principle and may not converge to global solutions. We would expect SVM method as a powerful tool for the prediction of molecular properties.