Psoriatic arthritis (PsA) is a systemic inflammatory condition associated with psoriasis. Despite considerable heterogeneity in clinical presentation, genetic studies and animal models support the notion that PsA is a distinct disease. We aimed to characterize the PsA genotype by gene expression profile and to research the effect in gene modulation of methotrexate (MTX) and TNF-inhibitors (TNF-I) in PsA-treated patients. Nine PsA patients, according to CASPAR criteria, and three healthy controls were recruited from an outpatient rheumatology clinic. Three out of nine PsA patients were naïve to treatment, three received TNF-I, and the remaining three were on MTX-monotherapy. Blood samples were collected and analyzed by human genome U95 Array-Affymetrix (GeneChip® instrument system). Identification of statistically significant differences between differentially expressed genes was determined by Mann-Whitney and t test (p < 0.05). The microarray profile identified a predominance of differentially expressed genes with an increased expression in baseline PsA patients: 115/12,000 genes were up-regulated and 13/12,000 down-regulated, as compared to healthy controls. The great majority were involved in inflammatory cells and pathways. In the biologic-treated patients, a higher number of down-regulated genes were expressed vs. the MTX patients, 161 vs. 33, respectively. This study shows that in PsA patients, TNF-I and MTX are able to modulate the gene expression in a synergistic and additive manner.