Isoflurane gas anesthesia is often used for immobilization of prairie dogs in field studies, laboratory research, and veterinary clinical purposes. The goals of this prospective study were to evaluate the effects of sternal versus right lateral recumbency on trends of selected physiologic parameters during isoflurane anesthesia in black-tailed prairie dogs (Cynomys ludovicianus). Fourteen adult, zoo-housed black-tailed prairie dogs were tested during the study. Animals were anesthetized using isoflurane and randomly placed in either sternal or right lateral recumbency to evaluate changes in trends of physiologic parameters, measured selectively every 30 min throughout a 60-min anesthesia period. Results were analyzed using linear mixed modeling. Right lateral recumbency resulted in a decrease in anion gap of about 4.6 mEq/L (95% confidence interval [95% CI]: 3.1–6.0, P < 0.001), whereas sternal recumbency resulted in a lower decrease of 2.1 mEq/L (95% CI: 0.7–3.6, P = 0.02). However, the absolute values at the beginning and at the end of the anesthesia time were not significantly different between the right lateral and sternal recumbency (all P > 0.57). Body position did not have any effect on any other variables, and most of the observed physiologic changes were due to the duration of anesthesia. Our results indicate no significant effect on trends of selected physiologic parameters between sternal recumbency and right lateral recumbency during 1 hr of isoflurane anesthesia in black-tailed prairie dogs.