The intercommunication between thyroid gland dysfunction in parents and aneuploid karyotype formation in offspring was studied using cytogenetic and immunogenetic approaches. It was determined, that increased risk for children being born with Down or Turner diseases depends upon a presence of following HLA-antigenes in parents, partcularly in motheritract. The intercommunication between thyroid gland dysfunction in parents and aneuploid karyotype formation in offspring was studied using cytogenetic and immunogenetic approaches. It was determined, that increased risk for children being born with Down or Turner diseases depends upon a presence of following HLA-antigenes in parents, particularly in mother's genome: B10, B40, B41, B51 and allele DQA*0301 of gene DQA of major histocompatibility complex. The presence of antigens B40, B51 and allele DQA*0301 was also associated with autoimmune thyroiditis. Thus, thyroid gland function disturbance, namely autoimmune thyroiditis can be considered as a risk factor of aneuploid karyotype formation.