OBJECTIVE: To explore the clinical phenotype and genetic diagnosis of a patient featuring secondary amenorrhea, breast dysplasia and mental retardation. METHODS: Peripheral venous blood samples were collected from the patient and her family members and subjected to G-banding karyotyping and single nucleotide polymorphism array (SNP-array) analysis. RESULTS: The patient was found to have a karyotype of 46,X,der(X)(12qter→ 12q22::Xq23→ Xpter)mat, her mother had a karyotype of 46,X,t(X;12)(Xpter→ Xq23::12q22→ 12qter;12pter→ 12q22::Xq23→ Xqter), while her father and brother were both 46,XY. SNP-array analysis suggested the patient to be arr[hg19]12q22q24.33(94 792 972-133 777 562)× 3, Xq23q28(108 786 070-155 233 098)×1. CONCLUSION The abnormal phenotypes of the patient can probably be attributed to the presence of Xq23-qter deletion and 12q22-qter duplication, both have derived from her mother's balanced t (X;12) translocation.