We assessed a simple, noninvasive method of monitoring transcutaneous partial pressure of CO2 (Ptcco2) in mice to determine whether it would provide an accurate and reproducible method to assess ventilatory depression in mice. To this end, Ptcco2 and Paco2 (partial pressure of arterial CO2) measurements were performed on isoflurane-anesthetized male C57Bl/6 mice breathing differing percentages of CO2 or fentanyl, a known ventilatory depressive drug. All doses of fentanyl produced a sharp increase in Ptcco2 values within 20 min with difference in Ptcco2 values between saline and all fentanyl groups being statistically significant (P < 0.0001). A good correlation between Paco2 and Ptcco2 values was established (r2 = 0.91). A Bland-Altman analysis likewise found that Ptcco2 measurements in the mice reliably and accurately reflected their Paco2 values. Therefore, under controlled conditions, Ptcco2 measurements were found to reliably reflect Paco2 values in mice. Consequently, the Ptcco2 method can be used as a means to rapidly and quantitatively assess the ventilatory depressive properties of a wide spectrum of drugs, under varying conditions in numerous mouse models.