Cardiac dysfunction leads to decreased organ perfusion. We aimed to measure cardiac and renal perfusion simultaneously with the use of (13)N-NH3-microPET in different rat models. Ten male Wistar rats underwent sham surgery (n = 5) or permanent coronary artery ligation to induce myocardial infarction (MI, n = 5). Eleven weeks later (13)N-NH3-microPET scan was performed to study the cardiac and renal perfusion. Cardiac perfusion was significantly reduced in MI group, directly correlated with ejection fraction and inversely correlated with MI size (r = 0.89; p < 0.001 and r = -0.86; p < 0.001 respectively). Renal perfusion showed a notional 17 % non-significant reduction in MI group when compared to sham (3.44 ± 0.40 vs. 4.12 ± 0.48 ml/g/min). There was a trend towards greater reduction of perfusion in cortical than medullar region. Cortex perfusion was negatively correlated with histological changes. (13)N-NH3-microPET may be a potential tool for evaluation of cardiac and renal functional and perfusion changes in presence of cardiac dysfunction in rat models.