An infant with congenital hypothyroidism (CH) is described who in the course of thyroxin replacement therapy developed cow's milk protein intolerance (CMPI) and subsequently coeliac disease (CD). The presence of these two pathologies interfered with the intestinal absorption of L-thyroxin (L-T4) and made the appropriate management of CH difficult. A male patient, formula fed from birth, was screened for CH at 5 days of age. CH was confirmed and L-T4 treatment (6.8 micrograms/kg/day per os) begun at 35 days of age. Seen after 3 weeks because of feeding problems and impaired growth and with a serum T4 concentration of 4.7 micrograms/dl and a TSH of 56 mU/ml, his replacement dose was increased to 12 micrograms/kg/day. One week later, the child was hospitalized because of vomiting, acidosis and shock. CMPI was diagnosed and the child began a diet with a hydrolyzed milk protein food. After 7 weeks the serum T4 improved to 11 micrograms/dl, the TSH decreased to 10 mU/ml, while maintaining the 12 micrograms/kg dose. After 2 months an oral challenge with cow's milk confirmed the diagnosis of CMPI with a concomitant decrease in serum T4 to 6.4 micrograms/dl, while TSH rose to 64 mU/ml. Weight and T4 levels normalised with CMPI diet. At 12 months of age the patient presented anorexia and impaired growth.(ABSTRACT TRUNCATED AT 250 WORDS)