Background/aim: In micropenis cases accompanied by external genital abnormalities such as hypospadias and cryptorchidism, infertility and spermatogenic failures have been reported to correlate with androgen receptor (AR) gene CAG and GGN repeat polymorphisms. While there is one study on isolated micropenis and CAG repeats, no study related to GGN repeats has been reported. We investigated the relation between CAG and GGN repeats in the AR gene with development of penis length in boys with isolated micropenis. Materials and methods: A total of 24 Turkish boys with isolated micropenis (<–2.5 SD) and 64 healthy controls who had normal basal serum gonadotropin levels were examined. Genotyping was performed by DNA sequencing of the patients and controls. Results: The distribution of CAG and GGN repeat lengths in our patients and controls was within the normal range and did not significantly differ between the patients and the controls. Conclusion: CAG repeat length in the AR constitutes one of multiple genetic factors relevant to the development of isolated micropenis, and the expansion of this repeat can be detected as a likely modifying factor. Moreover, the interactions of other genes that may be involved in the etiology of isolated micropenis with CAG and GGN repeats have to be taken into consideration.