We determine the prevalence and trends of open neural tube defects (ONTDs) during 1991 to 2019 at the “Dr. Juan I. Menchaca” Civil Hospital of Guadalajara (Mexico). Also, details of potential risks were obtained in 662 newborns, including those 143 patients with anencephaly and open spina bifida (OSB) classified as isolated (cases) and 519 controls. Data were analyzed using multivariable logistic regression. Among 267 201 live births during the study period, 336 were born with ONTDs, yielding an overall prevalence of 12.6 per 10 000. After folic acid (FA)‐related programs began in Mexico (2003‐2019), only OSB showed a decline of 20.6%. For anencephaly, associated risks included relatives with neural tube defects (NTDs) (adjusted odds ratio [aOR]: 67.9, 95% confidence interval [95% CI]: 11.3‐409.8), pre‐pregnancy body mass index (BMI) ≥25 kg/m2 (aOR: 2.6, 95% CI: 1.1‐6.0), insufficient gestational weight gain (aOR: 3.0, 95% CI: 1.3‐7.1), parity ≥4 (aOR: 3.2, 95% CI: 1.3‐7.7), and exposure to analgesic/antipyretic drugs (aOR: 9.0; 95% CI: 2.5‐33.0). For OSB, associated risks included consanguinity (aOR: 14.0, 95% CI: 3.5‐55.9), relatives with NTDs (aOR: 22.4, 95% CI: 4.5‐112.9), BMI ≥25 kg/m2 (aOR: 2.5, 95% CI: 1.6‐4.2), insufficient gestational weight gain (aOR: 1.9, 95% CI: 1.1‐3.1), and exposures to hyperthermia (aOR: 2.3, 95% CI: 1.2‐4.3), common cold (aOR: 6.8, 95% CI: 3.6‐12.7), and analgesic/antipyretic drugs (aOR: 3.6, 95% CI: 1.3‐10.0). Our high rate probably results from exposures to preventable risks, most related to FA, indicating a need for strengthening existing FA‐related programs in Mexico.