Down syndrome (DS, trisomy 21) results in intellectual disability. In DS the brain displays reduced cortical thickness, altered layer formation, and increased numbers of astrocytes and more prevalent choroid plexus cysts. Elucidation of the underlying molecular mechanisms and HSA21 genes responsible for intellectual disability in DS has been difficult because the bulk of brain formation in humans occurs prenatally. To address this we generated 45 and 140-day-old brain organoids from DS induced pluripotent stem cells (iPSC), and from DS iPSC in which the copy number of the HSA 21 gene APP was normalized as well as from their isogenic euploid controls. We subsequently subjected these to scRNAseq and a range of phenotypic analyses. We found that DS organoids show abnormal patterning of the cortical hem, a transient neuroepithelial structure in the dorsal telencephalon that forms the boundary between the developing cortex and the choroid plexus epithelium, and that constitutes the source of Cajal-Retzius cells that are known to orchestrate early circuit formation and structural development of the early cortex. Our data suggest these early brain developmental defects are due to altered Notch signalling downstream of APP and primary cilium alterations that affect SHH signalling. Our data highlight that human iPSC derived organoids provide a valuable platform for elucidating neurodevelopmental disorders and functional genomics.