Background: The purpose was to compare the levels and patterns of plasma cortisol and prolactin in patients with functional dyspepsia (FD) during a controlled laboratory experiment. Method: 25 patients (12 men, 13 women), aged 24–50, with recurrent FD, and 25 pair-wise gender- and age-matched community control subjects were studied at a gastroenterological laboratory in a Swedish university hospital. In an experiment, after a rest period, subjects were studied during a neutral interview and a stress interview. Before and during interventions, blood samples were drawn for later peptide analyses. The main outcome measures were the Gastrointestinal Symptom Rating Scale, heart rate, blood pressure, plasma cortisol and prolactin. Results: Mean plasma cortisol concentration correlated negatively with diarrhoea symptoms (partial correlation; p < 0.01). The level of plasma proclatin (µg/l) was significantly lower (paired t test; p < 0.01) in the patient group (mean = 3.34, CI: 2.75–3.93) compared to the control group (mean = 4.70, CI: 3.63–5.78). During the stress interview, prolactin increased significantly in both groups. When the whole sample was divided according to degree of reflux symptoms, those with high reflux symptomatology had lower prolactin (ANCOVA with covariates for group, gender, age, body mass index and smoking; p < 0.05). Conclusion: Plasma prolactin concentration was significantly lower in FD patients compared to a matched control group. A high degree of reflux symptoms was significantly associated with inhibition of the prolactin increase during a stress interview.