Objective To study the long-term effect of cerebral hypoxia and ischemia (HI) on the central acetylcholine (Ach) system and its treatments in neonatal rats. Methods Neonatal rats (7 days after birth) were subjected to permanent left common carotid artery ligation followed by 90 min of hypoxia with 10% oxygen at 36 ℃. The Ach level was measured immediately after HI (Group 1) and 14 days after HI (Group 2) using basic hydroxylamine chromatometry. In Group 3, basic fibroblast growth factor (bFGF) was injected (4μg ip) for 7 days immediately after HI. bFGF was given in the same way 3 days after HI in Group 4. The Ach level was measured 2 weeks after HI in Groups 3 and 4. Results The Ach level in the left globe decreased significantly immediately after HI (P<0.05). It did not return to normal until 14 days after HI. bFGF did not change the decreased Ach level obviously. Conclusions HI can damage the central Ach system of neonatal rat, moreover, the abnormality can persist for a long time. The bFGF has no protective effect on the damages of the Ach system .