Purpose Bariatric surgery is nowadays commonly applied as treatment for morbid obesity (BMI > 40 kg/m 2 ). As information about the effects of this procedure on a drug’s pharmacokinetics is limited, we aimed to evaluate the pharmacokinetics of CYP3A probe substrate midazolam after oral and intravenous administration in a cohort of morbidly obese patients that was studied before and 1 year post bariatric surgery. Methods Twenty morbidly obese patients (aged 26–58 years) undergoing bariatric surgery participated in the study of which 18 patients returned 1 year after surgery. At both occasions, patients received 7.5 mg oral and 5 mg intravenous midazolam separated by 160 ± 48 min. Per patient and occasion, a mean of 22 blood samples were collected. Midazolam concentrations were analyzed using population pharmacokinetic modeling. Results One year after bariatric surgery, systemic clearance of midazolam was higher 0.65 (7%) versus 0.39 (11%) L/min, mean ± RSE ( P  < 0.01), respectively and mean oral transit time (MTT) was faster 23 (20%) versus 51 (15%) minutes ( P  < 0.01), while oral bioavailability was unchanged (0.54 (9%)). Central and peripheral volumes of distribution were overall lower ( P  < 0.05). Conclusions In this cohort study in morbidly obese patients, systemic clearance was 1.7 times higher 1 year after bariatric surgery, which may potentially result from an increase in hepatic CYP3A activity per unit of liver weight. Although MTT was found to be faster, oral bioavailability remained unchanged, which considering the increased systemic clearance implies an increase in the fraction escaping intestinal first pass metabolism.