Using a prospective, randomized study design we demonstrate that midazolam sedation minimizes acidosis compared with physical restraint in captive juvenile estuarine crocodiles during handling or noninvasive procedures at preferred body temperature. A dose of midazolam (5.0 mg/kg) was administered intramuscularly into the forelimb of 20 male estuarine crocodiles weighing 2–3.5 kg. Their heart and respiratory rate and degree of sedation were monitored until recovery and then daily for 7 subsequent days. Blood samples were taken at 30, 60, 90, 180, and 360 min. We recorded lactate, partial pressure of carbon dioxide (CO₂), hematocrit, glucose, and blood pH. A second group (1.9–2.6 kg) was physically restrained for 5 min and the same parameters recorded. Physically restrained animals demonstrated elevated heart rate, respiratory rate, glucose, lactate, and anion gap compared with the midazolam-treated group. Physically restrained animals had lower pH, bicarbonate, and partial pressure of CO₂ compared with the midazolam-treated group. Behavior in the physically restrained group in the days following the study was disrupted, with reluctance to feed and bask, compared with midazolam-treated animals whose behavior was normal. We conclude that midazolam administered in the forelimb of captive estuarine crocodiles of 2–3.5 kg provides predictable onset and duration of sedation enabling physical examination, sample collection, and translocation of the animals with minimal disturbance to lactate, pH, and CO₂. Behavior following recovery appears normal.