Chronic inflammation is a well-established feature of sickle cell disease (SCD) even at steady state, and the degree of inflammation tends to correlate with disease severity. Elevated neutrophil count, as a reflection of the overall inflammatory state, has emerged as an indicator of poor prognosis and has been associated with adverse outcomes including stroke and early mortality. To further delineate the role of neutrophils in the pathogenesis of various complications and in overall disease severity in SCD, we analyzed the gene expression profiles of neutrophils from 5 patients with "severe" disease (>3 vaso-occlusive episodes [VOE] per year), 5 patients with "mild" disease (<3 VOE/year) and compared these to each other and to the gene expression profiles of neutrophils from 5 age and sex matched, healthy, non-sickle cell, African-American individuals. Granulocytes were separated from freshly collected venous blood using Histopaque (Sigma diagnostic) density gradient separation. Total RNA was extracted immediately after cell separation by using Rneasy Mini Kit (Qiagen). 2 micrograms of total RNA was converted to double stranded cDNA (ds-cDNA) by using SuperScript Choice System (Invitrogen). In vitro transcription was performed on the ds-cDNA using Enzo RNA transcript labelling kit. After the fragmentation, labeled RNA was hybridized to a set of oligonucleotide arrays (HG U133A, Affymetrix, Santa Clara, CA) and the data was analysed with the Microarray suite 5.0 software (Affymetrix). Out of the differentially expressed genes (314 genes for severe vs. control, 718 genes for mild vs control), those with greater than two fold expression were analysed with the geneMAPP software for localization into biological pathways. In general, a larger number of genes were differentially expressed between "mild" patients vs. control, compared to that between "severe" vs "mild" patients. Genes related to cellular proliferation, growth and maintenance, DNA repair, DNA replication, and cell cycle progression were expressed at significantly higher levels in SCD patients compared to controls. The most impressive finding was the significantly higher expression of genes leading to NFkB activation and inhibition of apoptosis: IAP-1 (increased 6.7 fold and 4.7 fold in mild and severe patients respectively), IkB (decreased 0.14 fold and 0.3 fold), Apaf-1 (decreased 0.4 fold in mild), and c-jun (decreased 0.4 fold in severe); Traf-2 (TNF receptor associated factor-2; increased 3.5 fold and 2 fold); genes in the MAPK signalling pathway: ERK-2 (increased 3.5 fold and 2-fold), MAP2K3 (increased 3.5 fold and 2 fold). These data show that neutrophils in SCD patients are activated with higher expression of genes in the TNF, MAPK, and NFkB pathways consistent with an inflammatory state. Delayed or inhibited apoptosis of neutrophils further maintains this inflammatory state even during the so-called "steady state" of the disease. We conclude that the analyses of gene expression in neutrophils can be a useful tool in identifying pathways and genes that distinguish SCD patients from controls and in differentiating mild and severe phenotypes.