The change in cell size and alterations in the distribution of cells at different phases of the cell cycle are indicators of change in cell homeostasis. In this study, the HEp-2 cell line cells were treated for 24 hours by two shapes of Gold nanoparticles (GNPs): Gold nanospheres (GNSs) and Gold nanorods (GNRs). The cytotoxic effect of GNPs was evaluated by different methods. The MTT assay revealed that GNPs have a cytotoxic effect on HEp-2 cells and the GNRs are more toxic than GNSs. Image morphometric analysis showed a decrease in the mean values of Nuclear Area Factor (NAF) of HEp-2 cells treated with GNPs when compared to control cells. We found that cell size decreased in cells treated with GNPs and most of the cells were in S-phase and decreased at G2-phase of the cell cycle when compared to control cells. Also, it was noted that in cells treated with GNSs the apoptotic features increased with increasing concentration from pre IC50 to post IC50, contrary to cells treated with GNRs the apoptotic features decreased with increasing concentration from IC50 to post IC50. Cell size and cell cycle distribution changed after treatment by GNPs. The GNRs may be more toxic than GNSs.