Serum non-organ-specific antibodies (NOSA) against nuclear, mitochondrial (AMA), smooth muscle, liver/kidney microsomal (LKM), reticulin, ribosomal, and organ-specific antibodies (OSA) against pituitary gland, gonads (testis, ovary) adrenal cortex, thyroid (thyroglobulin and microsomal), pancreas islet cells, gastric parietal cells and intestinal epithelial cells were evaluated in 45 patients with hypopituitarism (mean age 12.4 +/- 4.0 years). In 22 of them, 9 with isolated growth hormone (GH) deficiency (IGHD) and 13 with multiple pituitary hormone deficiency, MRI showed anterior pituitary hypoplasia with structural stalk abnormality and ectopic posterior pituitary. Twelve had isolated small anterior pituitary and IGHD and 11 had normal morphology of pituitary gland and IGHD. Controls were healthy age-sex-matched subjects. Thyroid antibodies were detected by a passive haemagglutination test while indirect immunofluorescence was used for the others. The auto-antibodies were found in 7/45 asymptomatic patients, a frequency not significantly different from that in controls; 5 were type NOSA and 2 type OSA. Pituitary antibodies were positive in 1 girl with IGHD and normal pituitary morphology. One girl developed hyperthyroidism during the follow up. Autoantibodies were equally distributed between the three groups and the frequency was not dissimilar from that in controls; this suggests that these patients are not at a higher risk of developing auto-immune disease, at least during the first two decades. CONCLUSIONS Pituitary insufficiency in children with different MRI features seems unlikely to be secondary to an auto-immune process.