Various factors including severe obesity or increases in intra-abdominal pressure during laparoscopy can lead to inaccuracies in end-tidal carbon dioxide (PETCO2) monitoring. The current study prospectively compares ET and transcutaneous (TC) CO2 monitoring in severely obese adolescents and young adults during laparoscopic-assisted bariatric surgery. Carbon dioxide was measured with both ET and TC devices during insufflation and laparoscopic bariatric surgery. The differences between each measure (PETCO2 and TC-CO2) and the PaCO2 were compared using a non-paired t test, Fisher's exact test, and a Bland-Altman analysis. The study cohort included 25 adolescents with a mean body mass index of 50.2 kg/m2 undergoing laparoscopic bariatric surgery. There was no difference in the absolute difference between the TC-CO2 and PaCO2 (3.2±3.0 mmHg) and the absolute difference between the PETCO2 and PaCO2 (3.7±2.5 mmHg). The bias and precision were 0.3 and 4.3 mmHg for TC monitoring versus PaCO2 and 3.2 and 3.2 mmHg for ET monitoring versus PaCO2. In the young severely obese population both TC and PETCO2 monitoring can be used to effectively estimate PaCO2. The correlation of PaCO2 to TC-CO2 is good, and similar to the correlation of PaCO2 to PETCO2. In this population, both of these non-invasive measures of PaCO2 can be used to monitor ventilation and minimize arterial blood gas sampling.