Non-invasive monitoring of breath ammonia and trimethylamine using Selected-ion-flow-tube mass spectroscopy (SIFT-MS) could provide a real-time alternative to current invasive techniques. Breath ammonia and trimethylamine were monitored by SIFT-MS before, during and after haemodialysis in 20 patients. In 15 patients (41 sessions), breath was collected hourly into Tedlar bags and analysed immediately (group A). During multiple dialyses over 8 days, five patients breathed directly into the SIFT-MS analyser every 30 min (group B). Pre- and post-dialysis direct breath concentrations were compared with urea reduction, Kt/V and creatinine concentrations. Dialysis decreased breath ammonia, but a transient increase occurred mid treatment in some patients. Trimethylamine decreased more rapidly than reported previously. Pre-dialysis breath ammonia correlated with pre-dialysis urea in group B (r(2) = 0.71) and with change in urea (group A, r(2) = 0.24; group B, r(2) = 0.74). In group B, ammonia correlated with change in creatinine (r(2) = 0.35), weight (r(2) = 0.52) and Kt/V (r(2) = 0.30). The ammonia reduction ratio correlated with the urea reduction ratio (URR) (r(2) = 0.42) and Kt/V (r(2) = 0.38). Pre-dialysis trimethylamine correlated with Kt/V (r(2) = 0.21), and the trimethylamine reduction ratio with URR (r(2) = 0.49) and Kt/V (r(2) = 0.36). Real-time breath analysis revealed previously unmeasurable differences in clearance kinetics of ammonia and trimethylamine. Breath ammonia is potentially useful in assessment of dialysis efficacy.