The relationship between end-tidal partial pressure of carbon dioxide (P_ETCO₂), arterial partial pressure of carbon dioxide (P_aCO₂), and blood pH in isoflurane-anesthetized raptors was evaluated. P_aCO₂ and pH were determined in serial arterial samples from isoflurane anesthetized birds and compared with concurrent end-tidal partial pressure of carbon dioxide measured with a Microstream sidestream capnograph. Forty-eight paired samples, taken from 11 birds of prey (weighing 416–2,062 g), were used to determine correlations coefficients between P_aCO₂ and P_ETCO₂, and between P_ETCO₂ and pH. Limits of agreement between P_aCO₂ and P_ETCO₂ also were calculated. Strong correlations were observed between P_aCO₂ and P_ETCO₂ (r = 0.94; P < 0.0001) as well as between P_ETCO₂ and pH (r = −0.90; P < 0.0001). However, the level of agreement between P_aCO₂ and P_ETCO₂ varied considerably. Low values of P_ETCO₂, ranging from 18 to 29 mm Hg, exceeded the concomitantly measured values of P_aCO₂ by an average of 6.0 mm Hg (6.0 ± 1.9 mm Hg; mean ± SD). Conversely, high values of P_ETCO₂, ranging from 50 to 63 mm Hg, were on average 7.6 mm Hg (7.6 ± 9.8 mm Hg) lower than values of P_aCO₂. In the 30 to 49 mm Hg range for P_ETCO₂, the difference between P_ETCO₂ and P_aCO₂ was on average 1.0 mm Hg (1.0 ± 8.5 mm Hg). These results suggest that the capnograph used provided a sufficiently accurate estimation of arterial partial pressure of carbon dioxide for birds weighing >400 g and receiving manual positive ventilation with a Bain system. In our study, the linear relationship observed between the pH and the end-tidal partial pressure of carbon dioxide suggested that the monitoring of end-tidal partial pressure of carbon dioxide also can be useful to prevent respiratory acidosis.