This retrospective study aimed to clarify the characteristics of bone maturation using longitudinal data in short-stature prepubertal children. Children with chronological ages (CAs) of 4.5-10.5 yr with nonfamilial idiopathic short stature (ISS, n = 95), familial ISS (FSS, n = 21), and short-stature children born small for gestational age (SGA, n = 23) were selected, of which 435 left-hand plain radiographic images were evaluated. Bone age (BA) delay was defined as BA minus CA. In the ISS group, there was a statistically significant difference in median BA delay among the CA groups (P < 0.001), as median BA delay gradually increased from 5-to 9-yr-old groups (−1.06 [range, −2.17 to 0.27] and −2.45 [range, −4.35 to −0.32] yr, respectively). In the FSS group, median BA delays were approximately −1 yr in all CA groups. In the SGA group, median BA delay gradually decreased from 7-to 10-yr-old groups (−1.96 [range, −2.99 to 0.56] and −0.04 [range, −2.44 to 0.92] yr, respectively), but with no significant difference (P = 0.647). The heavier weight of children with FSS and the probable earlier onset of adrenarche in children born SGA compared to those with ISS could have affected bone maturation.