Minipuberty is a period of increased reproductive axis activity in infancy, which seems to be implicated in the postnatal development of male genital organs. Impaired thyroid function during pregnancy is associated with an increased risk of prenatal, perinatal, and postnatal complications. The aim of this study was to investigate whether the presence of hypothyroidism during pregnancy modulates the course of male minipuberty. We compared three matched groups of male infants: sons of women with hypothyroidism uncontrolled or poorly controlled during pregnancy (group A), male offspring of women treated over the entire pregnancy with adequate doses of levothyroxine (group B), and sons born to women with no evidence of thyroid disease (group C). Salivary levels of testosterone, androstenedione, dehydroepiandrosterone sulfate, estradiol, progesterone, and 17-hydroxyprogesterone, as well as urine concentrations of FSH and LH, were assessed once a month in the first 6 months of life, and once every two months between months 6 and 12. Gonadotropin and testosterone levels during the first 6 months of life were lower in group A than in groups B and C. Differences in testosterone and gonadotropin levels were accompanied by similar differences in penile length and testicular volume. Concentrations of the remaining hormones did not differ between the study groups. The obtained results suggest that untreated or undertreated maternal thyroid hypofunction in pregnancy has an inhibitory effect on postnatal activation of the hypothalamic-pituitary-testicular axis and genital organ development in their male offspring.