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Fragile X syndrome (FXS) is the most common known genetic cause of male intellectual disability. A wide variety of medical problems has been reported in FXS syndrome including seizures, facial abnormalities, macroorchidism, and autistic disorders. Here we reported a 9-year-old boy with fragile X syndrome that was confirmed through karyotyping and mental retardation. Initially, he was diagnosed as hypothyroidism when he was 15 months old. However, due to unusual clinical presentation, we re-evaluated the patient according to his history and clinical findings. Subsequently, targeted laboratory tests were performed and the results were indicative for thyroxin-binding globulin (TBG) deficiency in our patient. Therefore, levothyroxine was discontinued and one month later, laboratory tests were repeated and his diagnosis confirmed. As inherited TBG deficiency might also be X-linked, FXS and TBG deficiency may be coincidental findings in the patient.