Pediatric obstructive sleep apnea (OSAS) is characterized by partial airway obstruction, alveolar hypoventilation, and elevated arterial CO2 (PaCO2). Thus, a reliable, practical method of estimating CO2 is needed for pediatric polysomnography. Therefore, we measured both transcutaneous CO2 (PtcCO2) and end-tidal CO2 (PetCO2) in 15 pediatric polysomnographic evaluations. Sleep state, the highest PtcCO2, and the highest PetCO2 were recorded for 5,159 thirty-second epochs. Although PtcCO2 and PetCO2 were available for 78.5 and 73.0% of epochs, respectively, at least one estimator was available for 92% of the epochs. One infant who would not tolerate a nasal sampling catheter had no PetCO2 data. For 13 of 14 studies there was a relatively constant difference between PtcCO2 and PetCO2. The difference between PtcCO2 and PetCO2 was within 4 mm Hg in 63.9% of 3,072 epochs. Across 14 studies, mean PtcCO2 exceeded mean PetCO2 by 2.8 ± 3.0 mm Hg, and it was within 4 mm Hg in 10 studies. In three subjects, PetCO2 was intermittently or consistently less than PtcCO2 because of tachypnea, increased physiologic dead space, or severe partial airway obstruction; in one subject PtcCO2 exceeded PetCO2 for undetermined reasons during one electrode application. The results of this study indicate that PtcCO2, as well as PetCO2, should be measured during pediatric polysomnography. By utilizing both PtcCO2 and PetCO2 there was a 70% reduction in the number of epochs that could not be assessed for hypoventilation. For an individual subject or electrode application there was a constant, and usually close, relationship, between PtcCO2 and PetCO2. PtcCO2 monitoring was particularly useful for children who would not tolerate a nasal sampling tube and for those with moderate to severe partial airway obstruction, tachypnea, or increased physiologic dead space in whom PetCO2 underestimated PtcCO2.