In organ transplantation, the determination of reliable parameters to assess ischaemic damage is essential to predict renal injury after preservation. The aim of this study was to assess renal medullary injury by 1H NMR (proton nuclear magnetic resonance) spectroscopy after preservation and reperfusion. Three experimental groups of pigs were examined during a 2-week period: control group (n = 4), Euro-Collins group (EC) (cold flushed and 48 h cold storage of kidney in EC and autotransplantation, n = 7), and University of Wisconsin (UW) group (cold flushed and 48 h cold storage of kidney in UW and autotransplantation, n = 7). Creatinine and urea were improved in the two cold stored groups. The most relevant resonances determined by 1H NMR spectroscopy after transplantation were those arising from citrate and acetate in urine and trimethylamine-N-oxide (TMAO) in urine and plasma. We demonstrate that graft dysfunction is associated with damage to the renal medulla as determined by TMAO release in urine and plasma. Conversely, citrate excretion can discriminate kidneys with favourable outcome. This study outlines the specific and beneficial impact of UW solution on renal preservation and suggests that 1H NMR spectroscopy is efficient both to detect ischaemic damage of preserved kidneys and to discriminate the preservation quality between different preservation solutions.