The purpose of this research was to clarify the significance of neutrophil CD64 expression in discrimination between infection and disease flare in patients with inflammatory autoimmune diseases. The study included 63 subjects, 20 healthy controls and 43 patients with inflammatory autoimmune diseases (24 with rheumatoid arthritis & 19 with systemic lupus erythematosus). The FC gamma receptor I (CD64 expression) on neutrophils was measured using flow cytometry. The intensity of CD64 expression on neutrophils was significantly elevated in patients with infections; 49.0 (13-205), and active autoimmune disease; 36.15 (12-133) compared to healthy controls; 5.35 (2.6-14) or patients with inactive disease; 7.5 (3.3-18). In the infectious disease group, expression of CD64 was significantly higher than in the active inflammatory disease group, while there was no significant difference between the group of patients with inactive inflammatory disease and healthy controls (P > 0.05). The sensitivity of CD64 bearing neutrophil intensity for detection of infection (using a cut off value of ≥43.5) was 94.4% and specificity was 88.9%. Neutrophil CD64 expression has a good sensitivity and specificity in differentiating infection from disease flare in patients with inflammatory autoimmune diseases. This assay could facilitate early and accurate diagnosis and greatly aid timely institution of appropriate treatment.