Although gonadal estrogens are known to facilitate the development of skeletal lesion in SHOX haploinsufficiency, controversy exists as to whether gonadal estrogens are disadvantageous to pubertal growth. To clarify this matter, we analyzed growth pattern in 31 Japanese patients with a normal karyotype and molecularly confirmed SHOX haploinsufficiency. The mean height SD score at the diagnosis of SHOX haploinsufficiency was similar between patients identified in childhood and those identified in adulthood (-2.7 +/- 0.8 [n = 15] vs. -2.4 +/- 0.7 [n = 16], P = 0.36), and was significantly lower in patients identified by the studies for short stature than in those ascertained by the familial studies of the probands both in childhood (-3.0 +/- 0.6 [n = 11] vs. -1.8 +/- 0.5 [n = 4], P = 0.0051) and in adulthood (-3.0 +/- 0.9 [n = 5] vs. -2.2 +/- 0.5 [n = 11], P = 0.040). Analysis of longitudinal paired growth data obtained in seven females showed a significantly different mean height SD score between childhood and adulthood (-2.3 +/- 0.5 vs. -2.9 +/- 0.8, P = 0.0060). The results imply that gonadal estrogens have a deleterious effect on pubertal growth in SHOX haploinsufficiency, and that the growth disadvantage is recognizable by longitudinal rather than cross-sectional growth studies.