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Background: The prevalence of obesity is increasing globally. Objectives: To evaluate whether gastric bypass surgery modifies the bioavailability and pharmacokinetic (PK) parameters of Omeprazole. Setting: Hospital Clínico San Carlos, Madrid, Spain. Methods: Controlled, open-label, bioavailability clinical trial in patients undergoing Roux-en-Y gastric bypass (RYGB). Healthy patients with obesity (BMI>35) were included and assessed for Omeprazole PK before RYGB and after (1 and 6 months). PK sampling was done at baseline and several times up to 12 h after drug dosing. Pre- and post-surgery parameters were compared using paired ANOVA or Wilcoxon tests, and Control vs. Cases using ANOVA or Mann Whitney tests. Given the post-surgery change in body weight, parameters were corrected by dose/body-weight. Results: Fourteen Case and 24 Control subjects were recruited, 92% were women (N= 35/38). In patients who underwent RYGB, Cmax was significantly reduced at 1 and 6 months after surgery compared with pre-surgery values (p=0.001). Regarding the AUC, the values are lower at 1 and 6 months after surgery than at baseline (p<0.001).The drug clearance was also increased in the first month after surgery. No differences were found between patients 6 months after surgery and Controls. Cmax and AUC corrected by dose/body-weight were significantly different between the baseline surgery subjects and Controls. Conclusions: Omeprazole bioavailability is reduced in patients with obesity at 1 and 6 months after RYGB. However, Omeprazole PK parameters 6 months after RYGB are similar to control subjects, and thus no dose correction is required after RYGB for a given indication.