In the toxicological testing of new small-molecule compounds, it is desirable to establish in silico test methods to predict toxicity instead of relying on animal testing. Since quantitative structure−activity relationships (QSARs) can predict the biological activity from structural information for small-molecule compounds, QSAR applications for in silico toxicity prediction have been studied for a long time. However, in recent years, the remarkable predictive performance of deep learning has attracted attention for practical applications. In this review, we summarize the application of deep learning to QSAR for constructing prediction models, including a discussion of parameter optimization for deep learning.