Hypertension is a major risk factor for cardiovascular diseases and is detrimental to several organs including the liver and kidneys. The flaxseed-derived polyunsaturated fatty acids including the omega-3 and omega-6 essential fatty acids have been shown to blunt the effects of hypertension. It is however, unclear whether the flaxseed, which is rich in these essential fatty acids, could improve the liver and kidney dysfunctions observed in the hypertensive condition. To test this, functional markers of the liver and kidneys, including aspartate aminotransferase (AST), alanine aminotransferase (ALT), blood urea nitrogen (BUN), uric acid (UA), creatinine, and renin were examined in hypertensive male Wistar rats fed a flaxseed diet. Normotensive rats maintained on a standard diet were rendered hypertensive with a daily administration of cyclosporin A (CYS) (25 mg/kg) for 4 weeks. Subsequently, hypertensive rats were either fed a standard diet alone or a flaxseed-supplemented standard diet (FLX; 10% W/W) for 8 weeks. Compared to normotensive rats, standard diet-fed hypertensive rats had significantly elevated blood pressure, altered lipid profile, and increased plasma levels of tissue markers measured immediately following the CYS treatment and thereafter at 4 and 8 week intervals. On the other hand, rats fed the FLX-supplemented diet had significantly lower blood pressure, an improved lipid profile and decreased tissue marker levels measured after 4 and 8 week durations. The data demonstrate for the first time the favourable effects of FLX in improving liver and kidney functions in the hypertensive condition. These effects are likely to be mediated by the alpha-linolenic acid (ALA) and linoleic acid (LA) contents of flaxseed oil due to its demonstrated ability to lower the blood pressure.