Introduction: Drug side effects are a relevant problem for patient safety and public health, and traditional methods have limitations in capturing complex patterns between clinical and pharmacological variables. Objective: To evaluate machine learning models to probabilistically predict multiple side effects associated with drug use. Materials and methods: A cross-sectional computational study was carried out with data from 1000 medications that included clinical condition, dosage and duration of treatment. Random Forest, Decision Tree, Support Vector Classifier and KNN were trained and optimized using Grid Search and an 80:20 split for training and testing. Chi-square tests and Principal Component Analysis were applied to explore associations and overlap between categories. Results: Significant associations were found between side effects and clinical condition (p < 0.05) and the drug administered (p < 0.05). The PCA showed a high overlap between categories, which justified a probabilistic approach. Tree-based models showed better performance (accuracy ≈ 0.35). Conclusions: Prediction of side effects is a multifactorial and non-deterministic problem; probabilistic machine learning models allow for estimating several plausible adverse events and can support clinical decision-making and pharmacovigilance.