Background: Circulating magnesium exists in the bound and in the free ionized form, that is biologically active. In kidney disease the relationship between ionized and total circulating magnesium is often altered. Little information is available on the influence of hemodialysis on the relationship between ionized and total circulating magnesium in end-stage kidney disease. Methods: Plasma total and ionized magnesium and the plasma ionized magnesium fraction were assessed before and after hemodialysis (dialysate magnesium content 0.75 mmol/l) in 46 patients with end-stage kidney disease and in a control group of 25 healthy subjects. Results: In patients plasma total (from 1.19 [1.05–1.33] to 1.10 [1.02–1.16] mmol/l; median and interquartile range) and ionized (from 0.71 [0.66–0.78] to 0.65 [0.63–0.69] mmol/l) magnesium significantly decreased during dialysis (control subjects: 0.82 [0.80–0.92], respectively, 0.57 [0.54–0.59] mmol/l). The plasma ionized magnesium fraction was significantly lower in patients both before (0.61 [0.58–0.64)] and after (0.60 [0.56–0.62]) hemodialysis than in controls (0.68 [0.65–0.70]). Conclusion: The study demonstrates a tendency towards a reduced circulating ionized magnesium fraction in end-stage kidney disease that is not corrected by hemodialysis.