Complex clinical presentation with diverse timing of particular symptoms may cause diagnostic difficulties, especially in children and adolescents. This paper presents diagnostic difficulties and pitfalls in 3 children with acquired primary hypothyroidism due to Hashimoto's thyroiditis (HT) presenting with unusual manifestations. We described 3 children with acquired primary hypothyroidism due to HT. One of our patients had musculoskeletal pain and was diagnosed and treated as having connective tissue disease. Another patient presented with chest pain, dyspnea, and swelling in the abdomen. She had a massive pericardial effusion (PE). Two patients had severe growth failure. A third patient with Down syndrome had a small PE. Her complaint was dyspnea during sleep. All patients improved with thyroxin therapy. Patients with hypothyroidism due to HT who have complicated clinical manifestations were misdiagnosed and mismanaged at childhood and adolescence. Growth failure is an important sign in children and adolescents. In the presence of complicated manifestations in children and adolescents, thyroid dysfunction must be considered in differential diagnosis.