Background: It is unclear whether Crohn’s disease (CD) is associated with skeletal disproportion in adulthood. Methods: Height (Ht), sitting height (SHt) and leg length were studied in 44 children (male: 22), 23 adults (male: 10) with childhood-onset (CO) CD and 26 adults (male: 9) with adult-onset (AO) CD with a median (range) age of 13.7 (10, 17.3), 21.5 (18, 32) and 31.0 (22, 40) years, respectively. Results: Adults with CO-CD had a median Ht standard deviation score (SDS) of –0.9 (–2.3, 0.0) compared to 0.6 (–0.8, 1.0) in those with AO-CD (p < 0.05). Compared to a normal population, men, but not women, with CO-CD also had lower median SHt SDS at –1.1 (2.5, –0.5) (p < 0.05). The expected positive association that is normally found between leg length and SHt SDS was not evident in the adults with CO-CD. Conclusion: Short stature in adults with CO-CD is more pronounced in men and may be associated with poor spinal growth.