The purpose of this study was to investigate the effects of chronic rapid eye movement sleep deprivation on cardiovascular system using blood levels of lipocalin-2, nitric oxide synthase-3, interleukin-6, and cardiotrophin-1. We included sixteen Wistar Albino rats of 300-350g weight in the study. To create a chronic rapid eye movement sleep deprivation, we used water tanks with platform including modified multiple sleep deprivation platforms, and we used water tanks with grid to grab for control group. We left 8 rats in water tanks with platform (study group) and 8 rats in water tanks with grid to grab (control group) for 21 days. Finally, we drew blood from the hearts of the rats, just before scarifying all the rats. We performed statistical comparisons of lipocalin-2, nitric oxide synthase-3, interleukin-6 and cardiotrophin-1 levels between the study group and the control group. The lipocalin-2, nitric oxide synthase-3, interleukin-6 and cardiotrophin-1 levels were 29.8ng/mL, 116.99ng/mL, 4.32ng/L and 33.26ng/L in the study group, respectively; and 122.74ng/mL, 85.74ng/mL, 3.23ng/L and 23.02ng/L in the control group, respectively. In the study group, mean lipocalin-2 levels were significantly lower (p=0.003) but mean cardiotrophin-1 levels were significantly higher compared with the control group (p=0.001). Mean interleukin-6 and nitric oxide synthase-3 levels did not significantly differ between the groups (p=0.135 and p=0.157). Our study showed that chronic rapid eye movement sleep deprivation might be associated with cardiovascular diseases owing to higher blood cardiotropin-1 levels in the study group, a novel biomarker that has been shown to indicate endothelial dysfunction, atherosclerosis and fibrosis in the cardiovascular system.