Introduction: Non-alcoholic fatty liver disease (NAFLD), cholecystitis and gallstones are important problems of public health which are associated with high fat diet intake and hypercholesterolemia. Capsaicin (CAP) is widely used in clinical practice. It can prevent obesity and lower blood lipids. Aim: To clarify the possible protective role of Capsaicin against the effects of high fat diet (HFD) on the liver and gall bladder using histological and immunohistochemical examinations and real time polymerase chain reaction (PCR). Material and methods: Thirty-two healthy adult male mice were separated into four groups. Control group: Animals were fed normal chow diet for 8 weeks. CAP group: Animals were fed normal chow supplemented with 0.01% CAP. HFD group: Mice were fed HFD for 8 weeks. HFD + CAP group: Animals were fed HFD supplemented with 0.01% CAP for 8 weeks. At the end of the study period, animals were weighed, anesthetized, blood samples were collected and abdomens were opened. Liver and gall bladder were removed for histological preparation. H&E, Masson, Cyclooxygenase-2 (COX-2) immunohistochemically-stained sections and ORO-stained frozen liver section were examined. Results: Ballooned and degenerated hepatocytes, thickened stratified hyperplastic gall bladder epithelium and inflammatory aggregations were observed in HFD group. Excess collagen fibers and strong positive COX-2 immunoreaction were also seen. Mean values of lipid profile levels, Peroxisome proliferator-activated receptor gamma (PPAR γ) and 3-hydroxy-3-methylglutaryl coenzyme-A (HMG CO-A) reductase gene expression group revealed an increase of very high significant difference from the control group. A decrease in these mean values was reported in HFD+CAP group which was of a very high significant difference from HFD and control groups. Normal hepatic and gall bladder architecture was markedly preserved in HFD+CAP and immunoreaction to COX2 was weak. Conclusion: CAP is suggested to have a great protective effect against HFD-induced histological changes in the liver and gall bladder through downregulating PPAR γ and HMG CO-A reductase gene expression and by acting as anti-fibrotic and anti-inflammatory agent