Introduction: Various trace elements are deficient in hemodialysis patients, but the relationship of such deficiencies with cardiac hypofunction is unclear. We examined the deficiencies of trace elements in the blood and hair of hemodialysis patients diagnosed with uremic cardiomyopathy and investigated cardiac hypofunction mechanism from myocardial tissue. Methods: Using blood samples, we measured 25 elements including Se, Mn, Cu, and Zn by high-resolution inductively coupled plasma (ICP) mass spectrometry and ICP emission spectral analysis. We also compared glutathione peroxidase (GSHPx) activation and radical formation potential between the uremic cardiomyopathy patient group (n = 22) and a control group with normal cardiac function (n = 30). Using myocardial tissue, we assessed the exacerbation of oxidative stress by 8-hydroxy-2-deoxyguanosine, 4-hydroxy-2-nonenal, and GSHPx staining and microcirculatory disorder by the perivascular fibrosis area ratio (PVFR). We also measured concentrations of elements in hair at the Super Photon ring-8 GeV (SPring-8) facility. Results: Compared with the control group patients, the uremic cardiomyopathy patients had lower selenium (99.7 ± 21.4 vs. 146 ± 23.3 ng/ml, p < 0.00001) and manganese concentrations (0.39 ± 0.15 vs. 0.60 ± 0.12 ng/ml, p < 0.001); they also showed decreased activation of GSHPx (121 ± 33 vs. 328 ± 44 μmol/min/L, p < 0.00001), an antioxidant enzyme involving selenium, with only selenium concentration correlating to left ventricular ejection fraction (p = 0.0009). Oxidative stress marker staining, radical formation potential in serum, and PVFR were all augmented in the uremic cardiomyopathic patients (p < 0.001). Conclusions: Selenium concentration decrease in the serum of hemodialysis patients may reflect a decrease in GSHPx activation, increasing oxidative stress, and precipitating a coronary microcirculatory disorder involved in the cardiac hypofunction seen in uremic cardiomyopathy.