Cardiopulmonary bypass (CPB) is widely used for cardiac surgery by virtue of its proven safety over the course of its use during the past half century. Even though perfusion is safer, incidents still occur. During the repair of a ventricular-septal defect in an 11-month-old infant, we experienced a critical incident related to the potential hazardous effect of volatile anesthetics on the polycarbonate connector of extra-corporeal circuit. The damage to the polycarbonate connector had occurred after spillage of isoflurane during the filling of the vaporizer, causing it to crack and leak. The incident was managed by replacement of the cracked connector during a temporary circulatory arrest. The patient was hypothermic and the time off bypass was less than 1.5 min. There were no neurologic sequelae, the patient made an uneventful recovery. In conclusion, the spillage of volatile anesthetics can cause cracks in the polycarbonate connector of the extra-corporeal circuit, leading to potentially interruption of CPB.