Background: Blood gas analysis (BGA), including measurement of ionized calcium, is performed routinely in patients with end stage renal disease on renal replacement therapy, especially when using citrate for regional anticoagulation. After installation of a new blood gas analyzer (RAPIDpoint (R) 405; BGA), we observed lower ionized calcium concentrations in a few patients without signs of hypocalcemia, whereas calcium concentrations were normal using a standard laboratory method. Pseudohypocalcemia was of limited duration and correlated with the short-term intake of sodium perchlorate monohydrate (Irenat (R)). Methods: We prepared dilution series from whole blood samples and stock solutions of calcium and perchlorate with different concentrations of ionized calcium and perchlorate. Measurement of ionized calcium concentrations was performed using two different blood gas analyzers (RAPIDpoint (R) 405; BGA and Roche AVL 9180; standard laboratory method). Results: After addition of different amounts of perchlorate, significant lower ionized calcium concentrations were measured with BGA compared to the standard laboratory method using either preparations from whole blood samples or stock solutions. The addition of potassium or methylene blue known to complex perchlorate had no effect on the concentrations of ionized calcium measured with BGA. Using different mathematical methods, a calculation of the "real" ionized calcium concentration from the value measured with BGA was not possible. Conclusions: Based on our experiments, we confirm the hypothesis that perchlorate can influence the measurement of ionized calcium by BGA. As the effect depends on the ion selective electrode that is used, it is advisable to test the blood gas analyzer with calcium and perchlorate solutions.