Trisomy 21 results in a group of clinical features known as Down syndrome (DS), the most common form of congenital developmental disability (Presson et al., J Pediatr 163:1163–1168, 2013; Shin, Pediatrics 124:1565–1571, 2009; Parker, Mol Teratol 88:1008–1016, 2010). The fundamental question for the field is how an extra copy of human chromosome 21 (HSA21) translates into the organ-specific pathologies in individuals with DS. Tissue and cells obtained from individuals with DS have been a primary source of analysis since before the discovery that trisomy 21 causes DS in 1959 (Lejeune, Ann Genet 1:41–49, 1959). Examination of primary tissue and cells established the features of DS in different organ systems. More recently, human pluripotent stem cells carrying trisomy 21 enable the generation of affected cell types and, importantly, provide insight into the development and degeneration of affected cell types. Further, exogenous and genetic manipulation of trisomy 21 cells facilitates identification of the contribution of genes and pathways to the pathogenesis of organ systems affected in DS.