Despite having identical CFTR genotype, individuals with F508 homozygous cystic fibrosis demonstrate significant variability in severity of pulmonary disease. This investigation utilized high-density oligonucleotide microarray analysis of nasal respiratory epithelium to investigate the molecular basis of phenotypic differences in CF by: 1) identifying differences in gene expression between F508 homozygotes in the most severe 20^th percentile of lung disease by FEV₁ and those in the most mild 20^th percentile of lung disease, and 2) identifying differences in gene expression between F508 homozygotes and age-matched non-CF controls. Microarray results from 23 participants (12 CF, 11 non-CF) met the strict quality control guidelines and were utilized for final data analysis. 652 of the 11,867 genes identified as present in 75% of the samples were significantly differentially expressed in one of the three disease phenotypes: 30 in non-CF, 53 in mild CF, and 569 in severe CF. An analysis of those genes differentially expressed by severity of CF lung disease demonstrated significant upregulation in severe CF of genes involved in protein ubiquination (p<0.04), mitochondrial oxidoreductase activity (p<0.01), and lipid metabolism (p<0.03). Analysis of genes with decreased expression in CF compared to controls demonstrated significant downregulation of genes involved in airway defense (p<0.047) and protein metabolism (P<0.048). This study suggests that differences in CF lung phenotype are associated with differences in expression of genes involving airway defense, protein ubiquination and mitochondrial oxidoreductase activity, and also identifies specific new candidate modifiers of CF phenotype.