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Objective The purpose of this study was to investigate medication adherence to oral chemotherapy medications and determinants of medication non-adherence to them among gastroenterological cancer patients. Methods A cross-sectional study was conducted on 117 consecutive, consenting, eligible patients visiting an outpatient clinic of university hospital in Japan. Good medication adherence was defined as taking 100% of the prescribed dose. Medication adherence was measured via self-report. We hypothesized that there was a significant relationship between medication non-adherence and the five factors defined by the World Health Organization: patient-related, socioeconomic-related, condition-related, treatment-related, and healthcare-system/provider-related factors. Multiple logistic regression models were used to identify factors associated with oral chemotherapy medication non-adherence. Results The proportion of patients showing good medication adherence was 56.4%. The multiple logistic regression analysis revealed that the determinants of medication non-adherence to oral chemotherapy medications included having a history of patient-caused treatment interruptions due to worsening of symptoms (adjusted odds ratio [AOR] = 9.59, 95% confidence interval [CI] = 1.38-66.47), having diarrhea (AOR = 3.25, 95% CI = 1.13-9.34), experiencing pain (AOR = 0.17, 95% CI = 0.05-0.55), taking oral chemotherapy medication every 8 h (AOR = 5.52, 95% CI = 1.71-17.81), and diminished sense of priority for medication (AOR = 1.40, 95% CI = 1.21-1.63). Conclusions This study suggests that many patients with gastroenterological cancer were non-adherent to oral chemotherapy medications. It might be necessary to conduct periodic screening and connect patients at a high risk of medication non-adherence to appropriate support.