Alterations in blood and tissue concentrations of trace elements in patients with chronic renal failure have been extensively investigated. Selenium, zinc and copper are elements which play an important role in biological systems as components of proteins, enzymes and antioxidants. The concentrations of selenium, zinc and copper were determined in the plasma, erythrocytes and whole blood of patients on regular hemodialysis (HD) and continuous ambulatory peritoneal dialysis (CAPD) treatment using the method of inductively coupled plasma mass spectrometry (ICP-MS). Analysis of isotopes 77Se, 66Zn and 65Cu was performed. Methodology presents the major limitation to valid studies on trace element levels in biological materials. One of the widely used contemporary techniques is ICP-MS. It is the most sensitive one and has a high dynamic range. The selenium concentration in the studied compartments (plasma 46.1 ± 3.0 vs. 78.0 ± 3.4 μg/l, p < 0.001; erythrocytes 90.4 ± 6.5 vs. 134.2 ± 7.6 μg/l, p < 0.01; whole blood 67.3 ± 3.1 vs. 106.4 ± 3.4 μg/l, p < 0.001) was significantly lower in HD patients compared to healthy controls. The same result was observed in plasma (63.2 ± 5.8 vs. 78.0 ± 3.4 μg/l, p < 0.05) and whole blood (82.7 ± 7.4 vs. 106.4 ± 3.4 μg/l, p < 0.01) from CAPD patients, but the selenium level of erythrocytes in CAPD patients was the same as in the control group (126.0 ± 8.8 vs. 134.2 ± 7.6 μg/l). The cooper content of erythrocytes was lower in HD patients than in controls (0.55 ± 0.02 vs. 0.66 ± 0.01 mg/l, p < 0.01) and CAPD groups (0.55 ± 0.02 vs. 0.68 ± 0.02 mg/l, p < 0.001). There were no differences in copper content in plasma (HD 1.02 ± 0.06; CAPD 1.11 ± 0.09; controls 1.02 ± 0.05 mg/l) and whole blood (HD 0.87 ± 0.04; CAPD 0.90 ± 0.05; controls 0.85 ± 0.02 mg/l) in HD and CAPD patients and healthy controls. The zinc concentration was increased in the whole blood of CAPD patients (6.68 ± 0.36 vs. 5.52 ± 0.11 mg/l, p < 0.001) and erythrocytes of HD (12.30 ± 0.23 vs. 10.11 ± 0.42 mg/l, p < 0.001), and CAPD groups (13.71 ± 0.56 vs. 10.11 ± 0.42 mg/l, p < 0.001) compared to controls. However, the plasma zinc concentration was lower in HD patients compared to blood donors (0.69 ± 0.03 vs. 0.92 ± 0.03 mg/l, p < 0.001) and CAPD patients (0.69 ± 0.03 vs. 0.95 ± 0.04 mg/l, p < 0.001). We did not find a significant increase in trace elements in whole blood after HD. These results suggest differences between plasma, erythrocytes and whole blood concentrations of the studied trace elements. The levels of trace elements are altered by HD and CAPD. A modern precise method with high accuracy, ICP-MS, which was used in our study, eliminated analytical errors and possible interferences.