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We studied the possible environmental factors in the origin of microcephaly by comparing the exposures of 109 infants with isolated microcephaly with those of two matched population controls, in addition to those of 812 patient controls (that is, infants with Down syndrome). Cases and patient controls were selected from the large population-based dataset of the Hungarian Case-Control Surveillance of Congenital Abnormalities registered between 1980 and 1996, whereas matched population controls were selected from the national birth registry. We found that there were more females than males among cases with isolated microcephaly. Evaluation of birth weight and gestational age indicated intrauterine growth retardation among microcephalic patients. The use of clotrimazole was higher among mothers in the matched population control group than among mothers of cases. Maternal use of a large dose (about 6 mg per day) of folic acid and more than 50 mg per day of iron during pregnancy was associated with a 40–50% decrease in microcephaly. Thus, the pharmacological doses of folic acid and iron may have some preventive effect against isolated primary microcephaly.