Cardiopulmonary bypass (CPB) circuits can significantly sequester intravenous anesthetics. Adsorption of medications by our institution’s standard circuit (Terumo CAPIOX FX05 oxygenator; noncoated polyvinylchloride tubing) has not been described. We prepared ex vivo CPB circuits with and without oxygenators. Medication combinations studied included midazolam (0.5 mg), fentanyl (50 µg), midazolam (0.5 mg) with morphine (0.5 mg), and midazolam (0.5 mg) with fentanyl (50 µg). Medications were administered after obtaining baseline samples. Samples were drawn at 2, 5, 15, 30, 60, 120, and 180 minutes, and analyzed for concentration of injected medications. Midazolam demonstrated no sequestration after 180 minutes. Fentanyl concentration at 180 minutes was lower with an oxygenator (52.7 ± 12.5 vs. 110.9 ± 12.0 ng/ml, P = 0.00432). More fentanyl was found in solution after 180 minutes when given with midazolam compared to fentanyl given alone in the presence of an oxygenator (101 ± 22.3 vs. 52.7 ± 12.5 ng/ml, P = 0.044). Less midazolam was present after 180 minutes when given with morphine compared to midazolam given alone in the absence of an oxygenator (1264.9 ± 425.6 vs. 2124 ± 254 ng/ml, P = 0.037). We successfully characterized the adsorption of various combinations of midazolam, fentanyl, and morphine to our CPB circuit, showing that fentanyl and midazolam behave differently based on other medications present.