Selected ion flow tube mass spectrometry (SIFT-MS) has been used for a detailed study of the daily variations in the acetone and ammonia content of the headspace above urine from a healthy female subject over the course of three separate menstrual cycles. Midstream urine samples were taken every morning prior to any food intake and the headspace subsequently analysed for a number of metabolites. Concurrent with the time of ovulation, a 3-to- 12-fold increase in the level of acetone in the urine headspace was observed. The successive peaks in acetone level and the subsequent return to baseline values were mirrored by similar increases in the ammonia levels, but these were a day out of phase. Interestingly, parallel breath analyses at ovulation showed no great increase in either acetone or ammonia above their normal morning levels, suggesting that these metabolites had been removed from the body during the night by the usual metabolic and physiological processes. The results of this study reveal what may be an important phenomenon at the time of ovulation and illustrate the potential and power of online SIFT-MS analysis in this area of research.