Background: Medicinal plants are of great importance to health of individual and communities. About 80% of the population in Uganda relies on traditional medicine because western-trained medical personnel are limited especially in villages. Most Ugandans use Hymenoxys odorato for medicinal purposes e.g. to treat colds, fever, coughs, anti-helminthes, locally used as tea, anti-allergy and also as an anti-venom to relieve snake bites. Method: A group of 25 male wistar rats of 150 g–210 g were kept for 14 days while being fed and treated with the extract. At 14^th day, anesthesia was given and blood samples collected by cardiac puncture for hematological and biochemical investigations. Serum was analyzed for Alkaline Phosphatase, Aspartate Transaminase and Alanine Transaminase while whole blood was used for complete blood count. The liver and kidney were removed and placed in 10% formalin to prepare for histology staining using haematoxylin and eosin technique. Results: The extract elevated hepatic biomarker enzymes i.e. ALP, ALT and AST. The increase was found to be significantly different (P > 0.05) at 400 and 500 mg/kg doses as compared to the control group. Histological sections of the liver showed distortion of liver cytoarchitecture, steatosis, necrosis of hepatocytes and congestion of the sinusoids at high doses 300, 400 and 500 mg/kg body weight. In the sections of the kidney, there was mild distortion of the integrity of the kidney with glomerular hypercellularity at high doses (400 and 500 mg/kg per body weight). Conclusion: Hymenoxys odorato aqueous extract has toxic effects on the liver and kidney of wistar rats. The effects were observed to be in a dose dependent manner.