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Summary Introduction Penile length is an important indicator of male sexual development. Scarce data were reported on penile length measurements in children comparing changes between prepuberty and puberty for the small penile issue with long-term follow-up. Objective The purpose of this study was to investigate the possibility of catch-up growth of the penile length of boys with a small penis in the long-term follow-up. Study design From April 2001 to December 2016, 27 boys who visited the outpatient clinic owing to a small penis, without any chromosomal anomalies and other genital disorder, were investigated retrospectively. Micropenis is defined as 2.5 standard deviations less than the mean stretched penile length (SPL) of age. Periodic penile length, testicular volume, hormonal levels (serum testosterone, luteinizing hormone (LH), and follicle-stimulating hormone (FSH)), and bone age were measured. Pubertal development was recorded by using the Tanner scale. The effect of hormonal therapy and the factors attributable to the increment of the penile length were evaluated. Results The mean age at the first visit was 9.8 years (5–12 years) and that at puberty was 12.6 years (10–16 years). The length of the penis at the initial visit was 4.0 ± 0.8 cm (2.5–6.0) and at puberty, 7.3 ± 1.8 cm (4.0–12.0). Nine patients diagnosed with micropenis no longer had a micropenis in puberty. The less the age-matched SPL, the more the increment of SPL that was observed (rho = - 0.548, P = 0.003). The mean increment of SPL in the hormonal therapy group (11 boys) and the non-hormonal therapy group (16 boys) was not statistically different (43.5 ± 22. 9% vs 41.5 ± 21.6%, respectively, P = 0.497). Discussion This study explains how much the growth of a small penis catches up in puberty. From the point of view of the increment of SPL, the increment was higher in boys who belonged to the smaller penis group. Hormonal therapy does not attribute to an increase in the length after long-term follow-up. Limitations of this study were its retrospective origin with a small number of patients in a single center. Conclusion Catch-up growth of the small penis at puberty was accomplished in most children with a small penis before puberty. Hormonal treatment was not significantly correlated with the penile length increment in the long-term follow-up.