To identify genetic expression of mandibular condylar cartilage during natural growth and under mechanical strain as a result of mandibular advancement. One hundred and forty four 35 days old female Sprague-Dawley rats were sacrificed on 8 different experimental days. Total RNA was extracted for oligonucleotide microarray gene chips containing 15,923 transcripts. Sixteen genes representing the chondrogenesis pathway were identified. Five of them were novel and have never been identified in mandibular condyles before. Quantitative analysis using real-time PCR revealed that these genes were involved in different stages in chondrogenesis and played an important role in condylar growth.