OBJECTIVE To evaluate the relationship between end-tidal partial pressure of CO(2) (ETCO(2)) and PaCO(2) in isoflurane-anesthetized harp seals. METHODS Three 5-month-old 25- to 47-kg harp seals (Phoca groenlandica). METHODS PaCO(2) was determined in serial arterial samples from isoflurane-anesthetized seals and compared with concomitant ETCO(2) measured with a side-stream microstream capnograph. Twenty-four paired samples were subjected to linear regression analysis and the Bland-Altman method for assessment of clinical suitability of the 2 methods (ie, PaCO(2) and ETCO(2) determinations). The influence of ventilation rate per minute (VR) on the ETCO(2) to PaCO(2) difference (P[ET-a] CO(2)) was examined graphically. RESULTS The correlation coefficient between the 2 measurements was 0.94. The level of agreement between ETCO(2) and PaCO(2) varied considerably. Values of ETCO(2) obtained with a VR of < 5 underestimated PaCO(2) to a greater degree (mean bias, -4.01 mm Hg) and had wider limits of agreement of -13.10 to 5.07 mm Hg (-4.01 mm Hg +/- 1.96 SD), compared with a VR of > or = 5 (mean bias, -2.24 mm Hg; limits of agreement, -7.79 to 3.30 mm Hg). CONCLUSIONS These results indicate that a microstream sidestream capnograph provides a noninvasive, sufficiently accurate estimation of PaCO(2) with intermittent positive ventilation at a VR > or = 5 in anesthetized harp seals.