The adverse effects of chlorpyrifos, cypermethrin, and imidacloprid on mitochondrial dysfunction and oxidative stress biomarkers were studied in rat liver. The liver deficiency was also confirmed by histological analysis and gel electrophoresis. Each insecticide was administered orally with five doses per week for 28 days to male albino rats at 1/50 of the LD50 per insecticide. The results demonstrated that the mitochondrial dysfunction was confirmed by a significant decrease in NADH dehydrogenase and ATPase activities. Oxidative stress biomarkers include malondialdehyde (MDA), and protein carbonyl content (PCC) were significantly increased. However, superoxide dismutase (SOD) and glutathione S-transferase (GST) as antioxidant enzymes were significantly decreased in the mitochondria of the rat liver. HPLC analysis showed a significant increase of the 8-hydroxy-2′-deoxyguanosine (8-OH-2DG) as a biomarker of the DNA damage in rat liver. In addition, the residue levels of 0.96 and 0.29 μg/mL serum were found for cypermethrin and imidacloprid, respectively. However, chlorpyrifos not detected using the HPLC analysis. Blue native polyacrylamide gel electrophoresis (BN-PAGE) analysis showed a change in the pattern and sequence of complexions of the electron transport chain in liver mitochondria with treatment by such insecticides. The hepatic histological examination also showed symptoms of abnormalities after exposure to these insecticides.