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The aim of this work is to describe the structure of the thymus, especially its medullary part, in children with congenital heart defects. It is known that development of the thymus and the heart is also influenced by neural crest cells. During the early development of the heart and the thymus cells proliferate and migrate to their primordia. It is known that inadequate cephalic neural crest contribution during development of pharyngeal pouch derivatives results in defective organogenesis of the face, the thymus, parathyroid glands and also the heart. We studied the structure of the thymus in children with congenital heart defects from 0 to 12 years of life at light microscopic and electron-microscopic levels. Thymuses of the patients were surgically removed in the Children’s Cardiocenter in Bratislava. The results of our study confirmed the differences in the medullary structures of thymuses with chosen diagnoses. Hassall’s corpuscles in the thymic medulla were various in size and also in structure and number. The special structures of the thymic medullary region in children with ventricular septal defects and defects of outflow of the heart were big cystic Hassall’s corpuscles. In comparison with a size of Hassall’s corpuscles in normal thymuses the size of Hassall’s corpuscles in studied thymuses suprisingly ranged between 100–250 μm.