Background The development of several disorders, such as cardiovascular diseases, diabetes and osteoporosis, has been linked to suboptimal dietary magnesium (Mg) intake. In this context, a number of studies have tried to investigate which Mg compounds are best suited for Mg supplementation. Results suggest that organic Mg compounds are superior to the inorganic Mg oxide in terms of bioavailability, but a reliable statement cannot yet be made due to systematic differences in the applied study designs. Methods This single-center, randomized, open, 2-period, 2-supplementation, 2-sequence, single-dose, cross-over study was conducted in 20 healthy male subjects of Caucasian origin to investigate and compare the bioavailability of Mg citrate, an organic Mg compound, and Mg oxide, an inorganic Mg compound. In order to reliably assess the bioavailability of both Mg compounds, subjects were supplemented with magnesium to saturate their Mg-pools before administration of each study product. The bioavailability of both Mg compounds was then assessed by measurement of the renally eliminated Mg quantity during an interval of 24 h after single-dose Mg administration (Ae 0-24h) as primary endpoint. Additionally, the Mg concentrations in a subset of leukocytes, in erythrocytes and in serum were measured on an exploratory basis. Results After administration, Ae 0-24h of magnesium was higher for Mg citrate than for Mg oxide. Ae 0-24h for both study products was compared by analysis of variance (ANOVA), revealing an adjusted mean difference of 0.565 mmol, which was statistically significant at the 5% level (95% confidence interval of 0.212 to 0.918 mmol, p = 0.0034). Besides, serum Mg concentrations were statistically significantly higher for Mg citrate than for Mg oxide at several time points after administration. No statistically significant difference was shown in intracellular Mg contents. Conclusions This study confirms former study results showing a higher bioavailability of the organic Mg compound Mg citrate compared to Mg oxide. It can be concluded that Mg citrate, similar to other organic Mg compounds, may be more suitable than Mg oxide to optimize the dietary magnesium intake.