Flow cytometry methods currently used for measuring neutrophil activation involve sample manipulation, which may result in cellular depletion and artifactual activation. To design a new methodology for measurement of neutrophil activation with minimal sample manipulation. Oxidative burst and CD 11b neutrophil expression were simultaneously assessed by a new no-lyse no-wash technique and a standard lyse-method in 10 pediatric patients with recurrent infections and two patients with chronic granulomatous disease (CGD). The new technique was based on nucleic acid staining to discriminate erythrocytes and debris without requiring physical separation. Both methods served equally to confirm or eliminate the diagnosis of CGD and leukocyte adhesion deficiency type 1. The values of baseline CD11b and oxidative burst obtained using the lysis method were significantly higher than those obtained by the no-lyse no-wash method. After activation, the lysis method resulted in higher neutrophil depletion (41%vs. 19%, P = 0.03). When compared with standard methods, neutrophil activation assessment by a no-lyse no-wash method resulted in lower neutrophil depletion and differences in oxidative burst and CD11b neutrophil values.