This study was designed to identify the relationship between vascularization and bone formation in the glenoid fossa during natural growth and functional appliance therapy. The temporal pattern of vascular endothelial growth factor (VEGF) expression and bone formation in the glenoid fossa during natural growth was identified and compared with that during forward mandibular positioning. We randomly divided 150 female Sprague-Dawley rats, 35 days old, into 10 experimental and 10 control groups. Appliances were fitted to position the mandible forward in the experimental groups. The rats were then killed at different times. Sections were cut and stained with anti-VEGF antibodies to evaluate VEGF expression, and with periodic acid and Schiff's reagent to evaluate new bone formation. Both VEGF expression and newly formed bone were measured by a computer-assisted image analyzing system. The results showed that, during natural growth and forward mandibular positioning, VEGF expression and new bone formation were highest in the posterior region of the glenoid fossa. There were significant increases of VEGF and new bone formation in the experimental groups compared with the controls. The highest amount of VEGF expression occurred before the highest amount of bone formation was reached. Forward mandibular positioning causes significant increases in vascularization and new bone formation in the glenoid fossa. A close correlation exists between vascularization and bone formation.