Introduction.Children with congenital hypothyroidism (CH) detected by newborn screening and adequately treated may have mild cognitive deficits. Objectives. To assess the intelligence quotient of children with CH and identify the presence of specific cognitive deficits. Population and methods. A group of 60 children with CH detected by newborn screening, who were aged 9-10 years old and received adequate treatment since their first month of life was selected and compared to a control group of 60 children without CH in the same age range. Inclusion criteria: children without concurrent diseases, who were attending school in a single shift, and whose parents had at least completed secondary education. The following tests were administered during individual interviews: the Wechsler Intelligence Scale for Children (third edition), the Rey complex figure test, the Woodcock-Muñoz revised test, the Conners Continuous Performance Test II, the Illinois Test of Psycholinguistic Abilities, the verbal fluency test, the Knox Cube Test, the Trail Making Test, the faces test, and the 5 digit test. The statistical analysis was done using Student's t tests (for independent samples) with Bonferroni's correction (p < 0.002). Results. Even within the normal average range, significant differences were observed between both groups in terms of total intelligence quotient and performance intelligence quotient (small and moderate effect sizes, respectively). In terms of performance, children with hypothyroidism had a significantly poorer performance in processing speed, reaction times, attention, cognitive flexibility, visuoconstruction, and long-term memory. No significant differences were found between both groups in the verbal area. Conclusions. Children with congenital hypothyroidism and without mental disability had mild cognitive deficits, which should be taken into account for a comprehensive patient care.