Early life stress including childhood maltreatment has been associated with reduced head circumference and/or brain size, cognitive, and academic deficits in children and adolescents. However, little is known about the effect of childhood maltreatment on height, especially in early adulthood. This study was designed to examine the association between confirmed cases of multiple or subtypes of childhood maltreatment and stunted growth in young adulthood controlling for perinatal and familial confounding factors. A total of 2661 (48.4% female) young adults from the Mater Hospital-University Study of Pregnancy (MUSP) had data on standardised height-for-age score measurement as part of physical assessment at the 21-year follow-up. Prospectively substantiated cases of childhood maltreatment, 0–14 years of age, were linked to the MUSP dataset. Ethical approval was obtained from the Human Ethics Review Committee of The University of Queensland and the Mater Hospital. Multiple regression analyses were performed to determine the effects of childhood maltreatment on height in young adults. Childhood physical or emotional abuse and neglect were significantly associated with a deficit in height in young adulthood after controlling for perinatal and familial confounders. Multiple incidents of childhood maltreatment also were associated with a deficit in height.