Objective: To determine whether blood levels of the brain-specific biomarker glial fibrillary acidic protein rise during cardiopulmonary bypass for repair of congenital heart disease. Methods: This is a prospective observational pilot study to characterise the blood levels of glial fibrillary acidic protein during bypass. Children <21 years of age undergoing bypass for congenital heart disease at Johns Hopkins Hospital and Texas Children's Hospital were enrolled. Blood samples were collected during four phases: pre-bypass, cooling, re-warming, and post-bypass. Results: A total of 85 patients were enrolled between October, 2010 and May, 2011. The median age was 0.73 years (range 0.01–17). The median weight was 7.14 kilograms (range 2.2–86.5). Single ventricle anatomy was present in 18 patients (22%). Median glial fibrillary acidic protein values by phase were: pre-bypass: 0 ng/ml (range 0–0.35); cooling: 0.039 (0–0.68); re-warming: 0.165 (0–2.29); and post-bypass: 0.112 (0–0.97). There were significant elevations from pre-bypass to all subsequent stages, with the greatest increase during re-warming (p = 0.0001). Maximal levels were significantly related to younger age (p = 0.03), bypass time (p = 0.03), cross-clamp time (p = 0.047), and temperature nadir (0.04). Peak levels did not vary significantly in those with single ventricle anatomy versus two ventricle repairs. Conclusion: There are significant increases in glial fibrillary acidic protein levels in children undergoing cardiopulmonary bypass for repair of congenital heart disease. The highest values were seen during the re-warming phase. Elevations are significantly associated with younger age, bypass and cross-clamp times, and temperature nadir. Owing to the fact that glial fibrillary acidic protein is the most brain-specific biomarker identified to date, it may act as a rapid diagnostic marker of brain injury during cardiac surgery.