The autopsy diagnosis of neonates with chondrodysplasias is often difficult due to the rarity of many of these conditions and to a complex classification scheme. Accurate diagnosis is essential for counseling of parents with one or more affected infants. Classification is currently based on radiological appearances and gross morphology. Following examination of two siblings with short rib polydactyly syndrome (SRPS) type I, we undertook to analyze the main problems in clinical pathological classification of chondrodysplasias. The problems identified are: variability in the constellations of morphological features that are used for diagnosis; insufficient radiological data being obtained at the time of autopsy; failure to preserve tissue appropriately for the necessary studies and lack of knowledge of the underlying abnormalities in most chondrodysplastic syndromes. It is anticipated that biochemical and molecular genetic abnormalities will eventually be discovered to reduce diagnostic uncertainty in the chondrodysplasias. Presently the diagnostic process is facilitated when frozen tissue is available for studies such as collagen, proteoglycan, and enzyme analysis and mRNA and DNA analyses.