Safety is a main reason for drug failures, and therefore, the detection of compound toxicity and potential adverse effects in the early stage of drug development is highly desirable. However, accurate prediction of many toxicity endpoints is extremely challenging due to low accessibility of sufficient and reliable toxicity data, as well as complicated and diversified mechanisms related to toxicity. In this study, we proposed the novel multitask graph attention (MGA) framework to learn the regression and classification tasks simultaneously. MGA has shown excellent predictive power on 33 toxicity data sets and has the capability to extract general toxicity features and generate customized toxicity fingerprints. In addition, MGA provides a new way to detect structural alerts and discover the relationship between different toxicity tasks, which will be quite helpful to mine toxicity information from large amounts of toxicity data.