In order to investigate the molecular effects of gold nanoparticles (GNPs) and cell interaction, after human dermal fibroblasts-fetal (HDF-f) treated with GNPs for 1, 4 and 8 h, the cytotoxicity was evaluated with methylthiazoltetrazolium (MTT) assay. Flow cytometry experiment was used to assess effects of GNPs on cell cycle and apoptosis. Differentially expressed genes in HDF-f treated with GNPs were obtained using gene expression profile microarray. The gene differential expression profile was analyzed by clustering, Gene Ontology (GO) and biological pathway. The results from these analyses were integrated to comprehensively interpret the data gained from microarray. It suggests that the exposure of HDF-f to GNPs might lead to the disturbance of cell cycle regulation, cellular oxidative stress and affect regulation of actin cytoskeleton, and other cellular activities such as cell adhesion, energy metabolism and signal transduction may be also affected. Compared with the cytotoxicological mechanisms induced by Ni2+ from our previous research and by GNPs from the present study, different underlying biological processes and gene regulations were found. The integration of microarray and bioinformatics analysis can provide a specific and efficient routine to discuss molecular effects of cellular response to biomaterials.