Positive contrast gastrointestinal (GI) studies are performed frequently in avian medicine to identify GI obstruction, luminal distension, and intracoelomic mass effects. However, repeated manual restraint and radiographic positioning may result in a stress-response and associated morbidity in birds, which can be attenuated by administration of sedative drugs. In mammals, many sedative drugs have been shown to affect GI transit times and motility. In this randomized, blinded, controlled prospective study, the effects of midazolam (M; 6 mg/kg IM) and midazolam-butorphanol (MB; 3 mg/kg each IM) on GI transit times were evaluated in 12 healthy cockatiels (Nymphicus hollandicus). Iohexol (20 mL/kg) was administered by crop gavage 15 minutes after induction of sedation, and fluoroscopic images were obtained at different time points. Both sedation protocols significantly affected GI transit times and motility, and the MB protocol had more pronounced effects. Overall median (range) GI transit times were 60 (30–120), 90 (30–120), and 120 (120–180) minutes for the control, M, and MB groups, respectively. Ventricular contractions were markedly reduced with both sedation protocols, while esophageal boluses were reduced only in the MB group. Visualization of the GI tract after iohexol administration was graded highest in the control group and poorest in the MB group. Our results show that commonly used sedative drugs have significant effects on GI transit time and motility in birds. Therefore, GI transit times obtained in sedated birds should not be compared to available reference transit times obtained from unsedated animals.