Patient adherence to medical treatment for dyspepsia is disappointing, whereas adherence is crucial for a proper evaluation of treatment. This prospective study used elements of the Integrated Change Model and Weiner's Attribution Theory to describe patients' important cognitions and their interrelationships regarding self-perceived adherence to short-term medical treatment for dyspepsia. Patient questionnaires measured the predictors before treatment and self-perceived adherence after treatment. Approximately one-quarter of the patients indicated that they were non-adherent (n = 347). Univariate and multiple linear regression analyses revealed several significant predictors that explained 44% of the variance in self-perceived adherence. Patients with a low educational level, patients who claimed to regularly forget their medication in general, patients with a low self-efficacy or a low intention were less likely to be adherent. These results may indicate targets for interventions designed to improve adherence to medical treatment for dyspepsia. For instance, asking about expected difficulties in taking acid suppressants (e.g. forgetfulness or medication use at weekends) and making action plans to overcome these difficulties (e.g. using reminders) may result in improved adherence rates. Such an approach may reach a substantial number of patients since one in five patients in our study experienced some difficulties in taking medication.