Recent progress in gas-sensing technology has enabled the rapid collection and highly sensitive analysis of skin gases associated with body odour. Skin gases can be collected less invasively, more continuously, and less consciously than blood or urine. Patients with end-stage kidney disease (ESKD) have a characteristic uremic odour that fades after initiating kidney replacement therapy. We investigated the potential for objectively and quantitatively evaluating the factors underlying uraemia. Skin gases were collected using a passive flux sampler placed on the forearm, with peak intensities measured using gas chromatography-mass spectrometry (GC/MS). We investigated the changes in skin gases obtained from the haemodialysis (HD) group before and after the first HD session of patients undergoing incident dialysis and compared them between the ESKD groups (HD and non-HD) and the healthy group. Thermal desorption enabled the collection of volatile molecules for 20 min using GC/MS preprocessing. Amongst 137 volatile molecules collected from the HD group (N = 5), 16 were detected in all patients. Aldehydes and alkanes were detected more frequently, and four volatile molecules, including 6-methyl-5-hepten-2-one, were detected in all participants in the ESKD (N = 11) and healthy (N = 7) groups. Benzaldehyde and undecanal showed significantly higher intensities in the ESKD group. Additionally, five unidentified volatile molecules were undetectable after dialysis, suggesting an association with the uremic odour. A comprehensive skin gas analysis technique has enabled the identification of volatile molecules related to ESKD. With a short sampling time, skin gas analysis has potential applications in clinical testing and telemedicine.