Celecoxib (Celebrex((R)), Pfizer) is a selective cyclooxygenase-2 (COX-2) inhibitor with chemopreventive and antitumor effects. However, it is now well known that celecoxib has several COX-2-independent activities. To better understand COX-2-independent molecular mechanisms underlying the antitumor activity of celecoxib, we investigated the expression profile of the celecoxib-treated COX-2-positive (Huh7) and COX-2-negative (HepG2) liver cancer cell lines, using microarray analysis. Celecoxib treatment resulted in significantly altered expression levels of 240 and 403 transcripts in Huh7 and HepG2 cells, respectively. Confirmation of the microarray results was performed for selected genes by semiquantitative RT-PCR. A pathway/functional analysis of celecoxib-affected transcripts, using ingenuity pathway analysis and exploring biological association networks, revealed that celecoxib modulates expression of numerous genes involved in a variety of cellular processes, including cell death, cellular growth and proliferation, lipid metabolism, and energy turnover. Some of these processes were common for both HCC cell lines and seem to be coupled with NF-κB signaling, while others were cell-specific and possibly linked to the presence or the absence of COX-2 activity in the corresponding cell line. Many novel genes emerged from our analyses that were not previously reported to be affected by celecoxib. Further studies on selected celecoxib-responsive genes will establish if they may serve as potential molecular targets for more effective therapeutic strategies in HCC.