A previously healthy 4 and a half year old boy presented to primary health care consultation. Due to red flags in the neurodevelopment evaluation, autism spectrum disorder is suspected and the child was oriented to child psychiatry. Seven months later, he is evaluated once again and, in addition to worsening neurodevelopmental delay and poor school performance, growth retardation is noted, as well as exponential weight gain. Prader Willi syndrome is suspected and the patient was referred to the pediatricians consultation. An analytical study was performed showing an exponentially elevated TSH (>750 mUI/L) associated with a decreased free T4 (0.24 ng/dL). A radiograph of the hand and fist revealed mineral bone age around two years and eight months. The autoimmune study revealed positive antithyroid peroxidase antibodies and antithyroglobulin antibodies and the diagnosis of autoimmune hypothyroidism was established. Levothyroxine was initiated with clinical improvement and return to linear growth. However, cognitive impairment was still present. Autoimmune thyroiditis is the most common cause of acquired hypothyroidism in pediatric age, although it is rare under the age of three. This condition, if not treated in a timely manner, can cause adult height loss and delayed neurodevelopment. The presented case illustrates the importance of including thyroid function in the study of children with growth retardation and unexplained weight gain. Changes in behavior and school performance should also alert to this diagnosis.