Background: Individuals with NR5A1 mutations encoding steroidogenic factor-1 (SF1) develop a phenotypically broad range of disorders of sexual development (DSD). Based on a literature review, we noted that hypoplastic seminiferous tubules and the emergence of Leydig cells with vacuolar cytoplasms are seen predominantly in the majority of individuals with NR5A1 mutations. Aim: The aim of this study was to address whether the histopathological characteristics of the testis can be a biomarker for 46,XY individuals with NR5A1 mutations. Design: In order to ascertain whether or not the histological features were the characteristics of NR5A1 mutations, we screened the testicular histology of 242 patients with 46,XY DSD and then subsequently assessed NR5A1 mutations. Result: Of 242 patients with 46,XY DSD, 6 patients matched histological testicular features: a reduced number of thin seminiferous tubules and focal aggregations of Leydig cells that contained cytoplasmic lipid droplets. All 6 patients had NR5A1 mutations. These histological features were distinct from those of other DSD. Thus, this unique testicular histology is useful for identifying NR5A1 mutations in 46,XY patients with DSD before puberty.