Morbidity prediction can be useful in improving the effectiveness and efficiency of medical services, but accurate morbidity prediction is often difficult because of the complex relationships between diseases and their influencing factors. This study investigates the effects of food contamination on gastrointestinal-disease morbidities using eight different machine-learning models, including multiple linear regression, a shallow neural network, and three deep neural networks and their improved versions trained by an evolutionary algorithm. Experiments on the datasets from ten cities/counties in central China demonstrate that deep neural networks achieve significantly higher accuracy than classical linear-regression and shallow neural-network models, and the deep denoising autoencoder model with evolutionary learning exhibits the best prediction performance. The results also indicate that the prediction accuracies on acute gastrointestinal diseases are generally higher than those on other diseases, but the models are difficult to predict the morbidities of gastrointestinal tumors. This study demonstrates that evolutionary deep-learning models can be utilized to accurately predict the morbidities of most gastrointestinal diseases from food contamination, and this approach can be extended for the morbidity prediction of many other diseases.