Obesity is an important risk factor for heart disease. This study investigated the effects of omega-3 (ω-3) on reversal of high fat (HF) diet-induced changes in the expression of the cardiac adiponectin and adiponectin receptors R1 and R2. Male rats were fed low-fat (LF; 10% energy from fat) or HF (45% energy from fat) for 16 weeks, LF-ω-3 or a HF-ω-3 (LF or HF for 16 weeks supplemented by ω-3 as 36 g/kg diet for the last 6 weeks, respectively) and a HF diet for 10 weeks to demonstrate HF effect before ω-3 administration. HF diet induced obesity, glucose intolerance, increased heart end systolic and diastolic volumes, decreased serum adiponectin, reduced expression of cardiac and adipose tissue adiponectin and adipo R1 & R2 with elevated serum tumour necrosis factor-α (TNF-α) compared to the LF diet. On the other hand, the HF-ω-3 group compared with the HF group had improved glucose tolerance (area under the glucose curve 837.14 ± 45.7 versus 1158.5 ± 69.8) and insulin resistance with a significant increase in serum adiponectin (4.22 ± 0.39 versus 2.82 ± 0.69 ng/ml) and a significant decrease in serum TNF-α (129.84 ± 13.63 versus 209.8 ± 16.42 pg/ml) and triglycerides independent of obesity. Also the data showed significant increases in the expression of cardiac and adipose tissue adiponectin and adiponectin R1 and adipose tissue adipo R2 as well as cardiac pAMP kinase with improvement in end-systolic and -diastolic volumes. These parameters were also improved compared to initial values in HF-10-week group. In conclusion, dietary ω-3 supplementation has a beneficial effect on fat-induced cardiac dysfunction and insulin resistance partly through increasing adiponectin and adiponectin receptors expression in heart and adipose tissue.