This paper is to provide a basis for the establishment of an early diagnostic system for hypoxic-ischemic encephalopathy (HIE) by performing segmentation and feature extraction of lesions on the MR images of neonatal babies with HIE. The segmentation on MR images of HIE based on the genetic algorithm (GA) combined with a pulse-coupled neural network (PCNN) were carried out. There were better segmentation results by using PCNN segmentation based on GA than PCNN segmentation with fixed parameters. The data suggested that a PCNN based on GA could provide effective assistance for diagnosis and research.