Human steroidogenic Factor 1 (SF1) is an orphan nuclear receptor that plays crucial roles in steroidogenesis and sex determination. SF1 mutations lead to 46,XY disorders of sex development (DSD), where chromosomally male individuals show mild (hypospadias), moderate (ambiguous genitalia) and severe clinical phenotypes (female external genitalia). While its steroidogenic roles are well-studied, the roles of SF1 in sex determination and testis development are poorly understood. SF1 initiates expression of SOX9 [SRY (sex determining region Y)-box 9] via a testis-specific enhancer (TESCO), enabling normal testicular development. SOX9 expression is then upregulated and maintained by synergistic transcriptional activation by SF1-SRY and SF1-SOX9 respectively on TESCO. We hypothesised that SF1 mutations in 46,XY DSD patients affect SOX9 transcription via TESCO. We assessed the ability of 20 SF1 mutants from DSD patients to activate TESCO. By performing in vitro reporter assays with a TESCO-luciferase construct and wild-type or mutant SF1, either alone or in combination with SRY or SOX9, we found that SF1 mutants showed defective activation of TESCO in 15 out of 20 cases. Synergistic activation of TESCO by SF1-SRY and SF1-SOX9 was also impaired. Analysis of protein structure and sub-cellular localisation of SF1 mutants predicted defects in DNA binding, ligand and co-factor interactions and nuclear translocation. A positive genotype-phenotype correlation was observed with levels of TESCO activity correlating with phenotype severity. This correlation implicates aberrant SF1-mediated transcriptional regulation of SOX9 in DSDs.