The study was designed to find out how oral ingestion of hyoscyamine fraction of D. stramonium seeds affect the DNA profiles patterns and expression of NeuroD1 gene in the hippocampus of adult Wistar rats. Fresh D. stramonium seeds were procured, identified, macerated and fractionated. Thirty-two (32) male adult Wistar rats weighed 200-250 grams were procured and divided into four groups comprised of control and three treatment groups for the study. The control received an equivalent bodyweight of normal saline, while the treatment groups received 200, 400 and 800 mg/kgbwt of hyoscyamine fraction for three weeks respectively. The animals were sacrificed, tissues harvested for histology, gel electrophoresis and gene expression studies. The fold changes were calculated and DNA profiles were determined using LabImage bio-imaging software. One-way ANOVA followed by Fisher’s multiple comparisons post-hoc test was used to obtain the difference in the expression of the gene across the groups using Minitab 17 (LLC., U.K.) statistical package software. P < 0.05 was considered statistically significant. There was a statistically significant downregulation (p = 0.001) in the NeuroD1 expression, increased DNA fragment size, decreased DNA migration distance and band volume, and necrosis of the dentate gyrus (DG) region in the hippocampus of the treated animals. In conclusion, oral ingestion of hyoscyamine fraction of D. stramonium seeds is toxic to the DNA profile patterns and expression of the NeuroD1 gene in Wistar rats.