An ion chromatographic method with conductivity detection for the simultaneous quantification of sodium, ammonium and potassium in exhaled breath condensate (EBC) was developed and validated. A factorial design was used to optimize the chromatographic conditions, which resulted in baseline separations of the cations within 6 min. The method requires no pre-treatment of EBC samples. The optimized method was used for the intra-individual screening of cations in EBC of 10 healthy volunteers. The LOQs were low (0.3, 0.1 and 0.2 microM for sodium, ammonium and potassium, respectively), compared with levels detected in healthy volunteers. The responses were linear with good precision, and samples could be stored for at least 10 weeks at refrigerating conditions.