Abstract Background Protein-bound uremic toxins are associated with poor outcomes in patients with chronic kidney disease. The aim of this study is to investigate the relationship between indoxyl sulfate (IS), a protein-bound solute, and 90-day mortality in patients with acute kidney injury. Methods Adults with hospital-acquired AKI (HA-AKI) were enrolled in this prospective cohort study between 2014 and 2015, according to the KDIGO creatinine criteria. The primary end point was all-cause death during follow-up. Results The mean serum IS level in patients with HA-AKI was 2.74 ± 0.75 μg/ml, which was higher than that in healthy subjects (1.73 ± 0.11 μg/ml, P