Abstract Background Acute kidney injury (AKI) is one of the most serious postoperative complications of cardiac surgery. The lack of early and powerful markers for AKI makes the morbidity and mortality still very high. HNL (Human neutrophil lipocalin)/NGAL (Neutrophil gelatinase-associated lipocalin) was recently shown as a novel biomarker for AKI after cardiac surgery. Methods Serial urine samples from 59 patients undergoing cardiac surgery were analyzed by polyclonal antibody based radioimmunoassay (RIA), monoclonal–polyclonal antibody based enzyme-linked immunosorbent assay (ELISA). Results We found 10 to 100-fold increases in urine HNL/NGAL levels in about half of the patients 2 h after termination of the operation and elevated levels in all patients 72 h post operation. The urine levels of HNL/NGAL showed a weak, but significant relation with kidney function as measured by plasma levels of cystatin C or creatinine. The 2 h-HNL/NGAL levels were positively correlated to extracorporeal circulation time ( p < 0001). The assays were well correlated, but had different clinical performances. Conclusions We confirmed that urine HNL/NGAL may be a useful early biomarker of postoperative kidney injury. The results indicate that the antibody configuration of the assay has an impact on the clinical performance of the assay.