A longitudinal, observational prospective panel cohort study of 61 patients lasting one year was undertaken. Explanatory variables included sociodemographic factors along with factors related to the underlying pathology as well as the protocol used and the type of treatment received. These variables were analyzed both individually and in combination to account for confounding effects and model interactions. A generalized estimating equation (GEE) model was constructed for each adverse effect. Associations were calculated as odds ratios (OR). Confounding variables related to drug tolerability were identified. Follitropin-alpha and cetrorelix exhibited the poorest safety profile. With respect to local adverse drug reactions (ADEs), the results obtained in our study point to statistically significant tolerability improvements for menotropin when administered in insemination. For gastrointestinal ADEs, ganirelix was the drug that showed the highest tolerability in in vitro treatments whereas follitropin-alpha showed the lowest tolerability in insemination treatments. Diverse factors related to assisted reproduction techniques (ART) influence the incidence of adverse effects. Each drug has a different safety profile with possible interactions depending on the type of assisted reproduction therapy used.