This prospective study characterizes the impact of positioning on the pulmonary volume and pulmonary atelectasis in Egyptian fruit bats (Rousettus aegyptiacus). The soft tissue appearance of atelectactic pulmonary parenchyma can obscure or mask pulmonary pathology. Soft tissue within healthy lung parenchyma caused by atelectasis can efface the margins of pathology, such as pulmonary metastasis or pneumonia, due to overlapping attenuation profiles. Pulmonary atelectasis is an unwanted side effect of anesthesia resulting from muscle relaxation and is exacerbated by high (80–100%) inspired oxygen supplementation during general anesthesia. Positioning can help minimize pulmonary atelectasis. Seven R. aegyptiacus received computed tomography imaging in suspended vertical (head-up) and inverted (head-down) positions that generated images in the dorsoventral plane. Vertically positioned bats had a significantly greater lung volume compared to inverted positioning (P = 0.0053). The nondependent portion of the lung apices in the vertically positioned bats had significantly more negative Hounsfield units (i.e. less dense tissue) than the dependent portions of the lung and was also less dense than both portions of the lungs in inverted positioned bats. Although not an intuitive positioning for bats, a vertical orientation generates less pulmonary atelectasis and a greater lung volume compared to bats positioned in a more natural inverted position. Despite physiologic adaptations to hang in an inverted position when not in flight, avoidance of inverted positioning during anesthesia and anesthetic recovery is recommended based on these findings.