Background: Functional dyspepsia is a heterogeneous condition and a uniform response to drug treatment is not likely. This may be the reason for the general failure of acid suppression in clinical trials in these patients. It may be more rewarding to identify true responders to drug treatment by a single subject trial. Aim: To develop and to test a novel single subject trial design (random starting day trial) in dyspeptic patients. Patients and methods: A total of 301 dyspeptic patients entered a 16-day trial. All patients received placebo for the first 4 days and switched to omeprazole at a randomized and blinded day between day 5 and day 14. Response was defined as a sustained ≥ 50% decrease in symptom score occurring in relation to drug shifting. Results: Spontaneous response varied between 0.3% and 10.6% per day, uniformly distributed over time. Overall, 53-61% of patients with organic dyspepsia had a symptom response in relation to shifting to active treatment, compared to only 23% of patients with functional dyspepsia. The only predictor of response was symptoms suggesting gastro-oesophageal reflux. Conclusions: A random starting clay trial may be a valuable tool to identify response to acid suppression in dyspeptic patients.