Background: Magnesium and calcium physiologic functions are closely related. Magnesium is primarily an intracellular cation, the action of which also involves maintenance of cellular ionic balance, while influencing calcium homeostasis by blocking calcium channels. The aim of this study was to compare the concentrations of magnesium and calcium in exhaled breath condensate (EBC) of children with asthma and gastroesophageal reflux disease (GERD).Subjects and methods: EBC was collected from 66 children aged 7–14 years (23 children with acute asthma, 17 children with GERD, and 26 healthy children).Determination of magnesium and calciumconcentrations was preceded by optimization and validation for low concentrations.Results: No difference was recorded for either magnesium or calcium concentration between study groups. However, the magnesium to calcium ratio was statistically significantly lower in both GERD and asthma children as compared with control group.Conclusion: Study results showed the magnesium to calcium ratio to be a statistically significantly better indicator of certain pathologic changes than absolute concentration of either ion. J. Clin. Lab. Anal. 23:34–39, 2009. © 2009 Wiley‐Liss, Inc.