Organ damage in systemic lupus erythematosus (SLE) patients is associated with decreased reactive oxygen species (ROS) production. ROS production was measured by flow cytometry after ex vivo activation of peripheral blood polymorphonuclear leukocytes (PMN) with phorbol 12-myristate 13-acetate. (A) The amount of ROS produced by PMN from patients with organ damage (Systemic Lupus International Collaborative Clinics/ACR damage index (SLICC/ACR-DI) ≥1) was compared with PMN from patients without organ damage (SLICC/ACR-DI = 0). (B) The amount of ROS produced by PMN from patients with (1) inactive disease (SLE activity index 2000 (SLEDAI-2 K) = 0) affected laboratory parameters, such as low complement and anti-double stranded DNA antibodies, but no clinical symptoms; (2) laboratory parameters only, and patients with clinical manifestations, for example, nephritis, rash and arthritis; and (3) clinical symptoms (P = 0,0654). (C) Phagocytosis of necrotic cell material, in the presence of serum and anti-nucleosome antibodies, by purified polymorph nucleated leukocytes (n = 40), was analysed using flow cytometry. The patients were divided based on organ damage (SLICC/ACR-DI) and their phagocytosis capacity is shown as% phagocytosing cells. The two-sided Mann-Whitney test was used to calculate the level of significance between two groups and Kruskal-Wallis test with Dunn’s multiple comparison test was used to calculate the level of significance between three groups. The line represents the median value of each dataset. MFI, mean fluorescence intensity.