Background:The aim of this study was to determine the effect of balloon atrial septostomy (Bas) on cerebral oxygenation in neonates with transposition of the great arteries (TGa). Methods: In term neonates with TGa, regional cerebral tissue oxygen saturation (r c sO 2 ) was measured using near-infrared spectroscopy (NIRs) for a period of 2 h, before Bas, after Bas, and 24 h after Bas. In neonates who did not require Bas on clinical grounds, r c sO 2 was measured within 24 h of admission and 24 h later. results: Bas was performed in 12 of 21 neonates. r c sO 2 increased from a median of 42% (before) to 48% at 2 h after Bas (P < 0.05), as did transcutaneous arterial oxygen saturation (spO 2 ) (from 72% to 85%, P < 0.01). r c sO 2 increased further during the next 24 h (from 48% to 64%, P < 0.05), whereas spO 2 remained stable. although beginning from a lower baseline (42 vs. 51%, P < 0.01), r c sO 2 was higher in neonates treated with Bas, as compared with neonates not treated with Bas, 24 h after the procedure (64 vs. 58%, P < 0.05); spO 2 was, however, similar between the two groups. conclusion: Bas improves cerebral oxygen saturation in neonates with TGa. complete recovery of cerebral oxygen saturation occurred only 24 h after Bas.