We aimed to determine the occurrence of pituitary dysfunction and additional malformations in patients with congenital nasal pyriform aperture stenosis (CNPAS) and to predict which patients are at risk of pituitary dysfunction. Among the 40 studied patients, hypothalamo-pituitary (HP) axis abnormalities were found in 16 patients (40%), with endocrine dysfunction (n = 9) and/or abnormal HP MRI findings (n = 15). A normal HP axis on MRI was highly predictive of normal endocrine function. Of the 40 patients, 31 had additional abnormalities in the cranio-facial area (n = 26), the brain (n = 12), the vertebrae (n = 5), the limbs (n = 4), the heart (n = 7) and the kidney (n = 3). Six patients had syndromic associations: VACTERL (n = 4), CHARGE (n = 1) and RHYNS (n = 1) syndromes. Craniofacial and brain malformations were more common in patients with HP axis abnormalities than in patients with normal HP axis. Familial history of midline defects and/or consanguinity were found in 30% of patients. In conclusion, HP axis abnormalities are frequent in patients with CNPAS and justify MRI of the brain early in life and clinical evaluation to screen for patients with pituitary insufficiency. CNPAS may be a genetically heterogeneous condition with a large phenotypic variability that shares common etiological mechanisms with the various forms of the holoprosencephaly phenotype.