Background It is unclear if amianthoid transformation (AT) of costal cartilage extracellular matrix (ECM) has an impact on the development of pectus excavatum (PE) and pectus carinatum (PC). Methods AT foci were examined in intrasurgical biopsy specimens of costal cartilages of children (8–17 years old) with PE (n = 12) and PC (n = 12) and in age-matching autopsy control samples (n = 10) using histological and immunohistochemical staining, atomic force and nonlinear optical microscopy, transmission and scanning electron microscopy, morphometry and statistics. Results AT areas were identified in the costal cartilage ECM in children with normal chest, PE and PC. Each type of the AT areas (“canonical”, “intertwined”, “fine-fibred” and “intralacunary”) had a unique morphological pattern of thickness and alignment of amianthoid fibers (AFs). AFs were formed via lateral aggregation of collagen type II fibrils in the intact ECM. Foci of the AT were observed significantly more frequently in the PE and PC groups. The AT areas had unique quantitative features in each study group. Conclusion AT is a structurally diverse form of ECM alteration present in healthy and pathological costal cartilage. PE and PC are associated with specific AT disorders.