The aim of this study was to evaluate the efficacy of the natural antioxidant astaxanthin in functional dyspepsia in different doses in a prospective and double-blind RCT. Patients with functional dyspepsia were divided into three groups with 44 individuals in each group (placebo, 16 mg, or 40 mg astaxanthin, respectively). Participants were asked to accept gastroscopy before treatment, together with the Gastrointestinal Symptom Rating Scale (GSRS) and SF-36 questionnaires. Urea breath test (UBT) was done before the treatment. The primary objective was to test the hypothesis that the antioxidant astaxanthin at two dosage regimens compared to placebo should ameliorate gastrointestinal discomfort measured as GSRS in patients with functional dyspepsia, who were either positive or negative for Helicobacter pylori, after 4 weeks of treatment. At the end of therapy (week 4) no difference between the three treatment groups was observed regarding mean GSRS scores of abdominal pain, indigestion and reflux syndromes. The same results were observed at the end of follow-up. However reduction of reflux syndrome before treatment to week 4 was significantly pronounced in the higher (40 mg) dose compared to the other treatment groups.