Depletion of antioxidants through consumption of a low antioxidant diet has been reported to increase neutrophilic airway inflammation and worsen symptoms of asthma. Using a nutrigenomics approach, this study explores the mechanisms of airway neutrophilic inflammation due to depletion of dietary antioxidants. Induced sputum samples were collected at baseline and after participants consumed a low antioxidant diet for 14 days. Genome-wide gene expression profiles were generated from sputum RNA samples from participants with a >10% change in sputum neutrophils using Illumina Humanref-8 expression microarrays. There were 104 genes differentially expressed following the dietary change. Upregulated genes were involved in the innate immune response and included the innate immune receptors TLR2, IL1R2, CD93, the signaling molecules IRAK2, IRAK3, and neutrophil proteases MMP25 and CPD. Downregulated genes included those involved in endogenous antioxidant defenses (GSTA1, GSTA2) and protease inhibition (SLPI, SERPINB3). Altered expression of five genes (TLR2, IRAK2, IL1R2, C20orf114, and SERPINB3) was confirmed using real-time polymerase chain reaction (PCR). These observations suggest that depletion of dietary antioxidants in asthma may result in upregulation of genes involved in the innate immune response. A diet low in antioxidants may be contributing to the development of neutrophilic asthma through activation of the innate immune response.