Diagnosis of acute kidney injury (AKI) in horses is difficult at the subclinical stage, due to nonspecific clinical signs. The aim of this study was to evaluate the concentrations of selected serum and urinary biomarkers in healthy horses, horses at risk of AKI, and those with clinical AKI. Thirty healthy horses, 30 horses at risk of AKI and 11 horses with clinical AKI and azotaemia were included in the study. Serum and urinary neutrophil gelatinase-associated lipocalin (NGAL) and cystatin C were measured using commercially available enzyme immunoassay tests. The median and (in parentheses) first and third quartile concentrations of selected biomarkers in healthy horses, horses at risk of AKI and horses with AKI were respectively as follows: serum cystatin C–0.25 (0.19–0.37), 0.23 (0.15–0.37) and 0.61 (0.37–1.13) mg/L; serum NGAL–50.5 (38.8–58.8), 51.1 (40.4–66.9) and 98.1 (59.4–128.2) ng/mL; urinary NGAL–20.7 (17.9–24.5), 32.3 (32.7–55.8) and 36.6 (26.8–89.9) ng/mL; and urinary cystatin C–0.1 (0.07–0.13), 0.13 (0.1–0.2) and 0.34 (0.22–0.37) mg/L. There were significant differences in the concentration of all biomarkers between the healthy and AKI-affected horses. Horses with AKI all had biomarker concentrations higher than the healthy horses. None of the biomarkers made azotaemia recognisable in all affected horses. The obtained results indicate the need to create a serum and urinary biomarker panel to detect AKI.