We herein report the case of a woman with aniridia and with a heterozygous PAX6 mutation. Pax6 is a transcription factor involved in the development of several organs, including the eye, pancreas and pituitary. The patient had been diagnosed with aniridia in childhood and was found to have impaired glucose tolerance with a heterozygous PAX6 mutation 12 years prior to the current admission. Hormone stimulating tests revealed a slightly impaired pituitary function, including subtle hypogonadotropic hypogonadism and borderline growth hormone (GH) deficiency. The present case is the first report of a slightly impaired pituitary function in an aniridia patient with a heterozygous PAX6 mutation.