Objective To determine the effect of fraction of inspired oxygen (FiO(2)) on intrapulmonary shunt fraction as measured by F-shunt in ponies during isoflurane anaesthesia. Study design Prospective, randomized clinical study. Animals A group of 23 adult Shetland ponies undergoing a total of 32 anaesthetic procedures. Methods Ponies were premeditated intravenously (IV) with detomidine (0.01 mg kg(-1)) and either morphine (0.1 mg kg(-1)) or butorphanol (0.02 mg kg(-1)). Anaesthesia was induced with ketamine (2.2 mg kg(-1)) and midazolam (0.07 mg kg(-1)) administered IV. Ponies were randomly allocated to maintenance of anaesthesia with isoflurane in oxygen (group TH; FiO(2) = 0.95) or a mixture of oxygen and medical air (group TL; FiO(2) = 0.65); all ponies were given a constant rate of infusion of detomidine. Animals were mechanically ventilated to maintain PaCO2 between 40 and 50 mmHg. Arterial blood gas analysis was performed every 30 minutes. The F-shunt equation was calculated for each time point TO, T30, T60 and T90. Data were analysed using linear mixed model analysis and presented as mean +/- standard deviation (p < 0.05). Results PaO2 was greater in group TH than in group TL (TH: 406 +/- 90, 438 +/- 83, 441 +/- 69 and 464 +/- 53 mmHg versus TL: 202 +/- 90, 186 +/- 84, 172 +/- 85 and 191 +/- 98 mmHg at TO, T30, T60 and T90, respectively; p < 0.0001). In TH, F-shunt was < TL. Significant differences were found at T60 (TH: 13.2% +/- 4.3 versus TL: 19.4% +/- 8.3; p = 0.016) and T90 (TH: 11.7% +/- 3.5 versus TL: 18.6% +/- 9.5; p = 0.036). Conclusions and clinical relevance Our findings do not support a beneficial effect of using a reduced FiO(2) to improve oxygenation in anaesthetized and mechanically ventilated Shetland ponies.