It is difficult clinically to measure relative blood flow to each lung. We hypothesized that uni-lung % blood flow is linearly related to % carbon dioxide excretion (VCO2). In a canine model of acute unilateral lung injury, we measured uni-lung flow with ultrasonic flow-probes, and uni-lung VCO2 with two separate metabolic monitors utilizing split lung ventilation following thoracotomy. Relative flow to the lungs was altered by inflating a pulmonary artery catheter balloon in one of the lungs under conditions of normal lung function and following induction of acute lung injury. There was a significant linear relationship between % blood flow and % VCO2 under all conditions (R = 0.83, p < 0.001, ANOVA). The slopes were identical for the injured lung and the contralateral control lung, although these slopes differed from their respective baseline values. We conclude that by measuring uni-lung % VCO2, one may trend changes in % flow to either lung in patients with split lung ventilation with or without unilateral lung disease.