Developmental defects in children constitute a significant clinical problem, affecting both the functioning of the stomatognathic system and the quality of life of patients and their families. Disorders occurring in the course of genetic and dysmorphic syndromes are particularly significant. Each of these conditions has a distinct clinical picture, but a common denominator is the presence of anomalies in the craniofacial region, teeth and soft tissues of the oral cavity, which can lead to impaired functions of respiration, swallowing, chewing and speech. The analysis of these defects is crucial for early diagnosis, treatment planning and the prevention of complications. Proper understanding of the pathogenetic mechanisms and characteristics of morphological changes enables an interdisciplinary approach to therapy, encompassing pediatrics, maxillofacial surgery, orthodontics, prosthetics, speech therapy and rehabilitation. Orthodontic and prosthetic treatments play a special role, improving chewing function, articulation and facial aesthetics, thus influencing the child’s psychosocial development. The aim of this article is to discuss the most common defects in the oral cavity and the maxillofacial region in children with Treacher Collins syndrome (TCS), ectodermal dysplasia syndrome, Pierre Robin syndrome (PRS) and trisomy 21 (Down syndrome), and to present the possibilities of orthodontic and prosthetic treatment in this group of patients.