The pathogenesis of craniosynostosis is complex. Apoptosis, a process of cell deletion that occurs without inflammation, is important in limb morphogenesis and may play a role in cranial suture patterning. The in vivo rate of apoptosis in craniosynostosis remains undefined. The purpose of this study was to compare the rate of apoptosis between prematurely fused sutures and open sutures in patients with craniosynostosis using histological stains. Cranial sutures were harvested from 10 children with craniosynostosis at the time of cranioplasty. One closed suture and one adjacent open suture were removed, processed, and stained with hematoxylin and eosin stains. Apoptosis was identified based upon characteristic nuclear morphology. The apoptotic index (percentage of cells undergoing apoptosis) was calculated for each specimen and was compared between fused and open sutures. A zone of apoptosis was observed to occur along the osteogenic front in open sutures. Open sutures had a significantly higher apoptotic index (7.35%) than did fused sutures (1.43) (p<0.05). We found a higher rate of apoptosis in open sutures than in closed sutures in patients with craniosynostosis. These findings support the hypothesis that apoptosis may serve to reduce the rate of suture fusion and thus prevent premature suture fusion.