Background: PFAPA syndrome is a non-mendelian autoinflammatory disease of unknown etiology characterized by Periodic Fever, Aphthous stomatitis, Pharyngitis, and cervical Adenitis. In typical cases, attacks begin before the age of five and occur every 2-8 weeks with striking periodicity. We have previously profiled the blood cells and serum cytokine levels in a cohort study of patients with PFAPA (Brown et al, BMC Pediatric 2010:10, 65) and the purpose of the present study was to investigate neutrophil function during the febrile and afebrile state in the same cohort. Methods: Neutrophils (PMN) were isolated from blood collected from twelve PFAPA patients during febrile and afebrile phase (median age of 3.5 yrs). PMN apoptosis was assessed by annexin V staining, production of reactive oxygen species (ROS) by luminol/isoluminol-amplified chemiluminescence, MPO quantity by ELISA, and degranulation/priming as surface expression of CD11b and L-selectin by flow cytometry. Results: We found a significantly increased intracellular (ic) production of ROS in response to phorbol myristate acetate in PMN during the febrile phase, as compared to cells from the afebrile phase and controls. No differences were found in MPO quantity between the samples, indicating that the increase in icROS-production was due to increased NADPH-oxidase activation. We also found decreased spontaneous apoptosis in PMN during the febrile phase of PFAPA, while apoptosis was instead increased during the afebrile phase. Increased expression of CD11b indicated that the PMN were slightly primed during the febrile phase, supported by increased oxidative response to galectin-3, a priming-dependent process. Conclusion: Alterations in PMN function, e.g., icROS-production, priming and spontaneous apoptosis, may give mechanistic clues to the so-far undefined etiology of the PFAPA syndrome.