Ts65Dn, a well-characterized animal model for Down syndrome, has three copies of the distal end of mouse chromosome 16 and therefore has segmental trisomy for orthologs for nearly half of the genes located on human chromosome 21. Ts65Dn mice have learning and memory impairments, especially in tasks involving the hippocampus. Previous studies have shown that older adult Ts65Dn mice have structural abnormalities in the hippocampus including fewer granule cells in dentate gyrus and more pyramidal cells in the CA3 subfield of cornus ammonis. However, it is not clear whether those changes are secondary to the age-related neurodegeneration of the basal forebrain cholinergic neurons that project to the hippocampus or if they originate earlier during hippocampal development. To address this question, we performed a quantitative study of the hippocampal volume and the numbers of granule cell and pyramidal neurons in young (postnatal day 6, P6) and adult (3-month-old) mice using the optical fractionator method. At P6, Ts65Dn mice had 20% fewer granule cells in dentate gyrus than did euploid littermates. Similarly, compared to euploid, P6 trisomic mice showed an 18% reduction in mitotic cells in the granule cell layer and the hilus, where granule cell precursors divide to generate the internal granule cell layer. Granule cell hypocellularity persists in 3-month-old Ts65Dn mice before the onset of cholinergic atrophy. The hypocellularity seen in the trisomic adult hippocampus originates early in development and may contribute to specific cognitive deficits in these mice.