A unique case of gonadal agenesis and rudimentary müllerian duct development in association with a 46,X,i(Xq) karyotype is reported. The patient presented with short stature and subtle features of Turner syndrome. Endocrine evaluation revealed elevated gonadotropins and cytogenetic findings from both peripheral blood leukocytes and skin fibroblasts were consistent with a 46,X,i(Xq) karyotype. Laparoscopy revealed both uterus and gonads to be absent. Developmental failure of the müllerian system in association with gonadal agenesis in a patient with 46,X,i(Xq) has not been previously reported. The basis for müllerian duct regression in this patient remains unclear. Recommendations for treatment are made.