A pilot study evaluated neutrophil activation in autoimmune kidney diseases by measuring blood heparin-binding protein (HBP) in 70 patients, including 20 with anti-neutrophil cytoplasmic antibody (AAV)-associated vasculitis, 17 with membranous nephropathy (MN), and 17 with minimal change disease (MCD)/focal segmental glomerulosclerosis (FSGS). The control group consisted of 18 patients with sepsis, 20 on hemodialysis and 20 healthy volunteers. Blood HBP levels were significantly increased in all autoimmune kidney diseases, highest in AAV and lowest in MCD/FSGS. Unlike NGAL, HBP was not affected by estimated glomerular filtration rate (eGFR) and was independently correlated with blood neutrophil count. Its sensitivity was higher than that of NGAL, neutrophil count, and C-reactive protein. In AAV, HBP was associated with hematuria and its levels decreased significantly after remission, whereas in MN and MCD/FSGS, increased HBP was associated with higher proteinuria. In patients with autoimmune kidney diseases, there was a positive correlation between HBP in blood and urine. Blood HBP is an eGFR-independent marker of neutrophil activation, which is widespread in these diseases.