Atherosclerosis is a leading cause of death due to cardiovascular diseases worldwide. Accumulation of lipids in the big arteries triggers inflammatory markers, such as tumor necrosis factor (TNF)-α and interleukin (IL)-6, that by turn induce endothelial injury. It is mandatory to find a prophylactic medication for this disease, especially from natural resources to avoid the side effects of drugs. Chia seeds and Flaxseed oil are natural herbal, each separate administration showed good results in ameliorating hyperlipidemia and reducing atherosclerosis inflammatory response. The combination of those two natural resources could have a synergistic prophylactic effect and better lessening of atherosclerosis and it is the aim of this study, to investigate the potential prophylactic effect of a combination of Chia seeds and Flaxseed oil on a rat model with induced atherosclerosis through high-fat diet. Using chemical and immunohistochemical techniques to explore the effect of this combination on serum lipid parameters level and to study the protein expression of inflammatory markers; IL6 and TNFα in aortic tissue with or without the administration of Chia seed and Flaxseed oil each separate or combined. Significant changes in the lipid profile and inflammatory markers were demonstrated in the combined group, where it improved lipid parameters, body weight, and mean arterial blood pressure, it also ameliorated aortic inflammation compared to Chia seeds or Flaxseed oil alone. This could be guidance to use Chia seeds combined with Flaxseed oil as prophylaxis against atherosclerosis to limit its unfavorable effect.