In this paper, we propose a multi-parametric in vitro study of the cytotoxicity of gold nanoparticles (GNPs) on human endothelial cell (HUVEC). The cytotoxicity is evaluated by incubating cells with six different GNP types which have two different morphologies: spherical and flower-shaped, two sizes (∼15 and ∼50 nm diameter) and two surface chemistries (as prepared form and PEGylated form). Our results showed that by increasing the concentration of GNPs the cell viability decreases with a toxic concentration threshold of 10 pM for spherical GNPs and of 1 pM for flower-shaped GNPs. Dark field images, flow cytometry and spreading test revealed that flower-shaped GNPs have more deleterious effects on the cell mechanisms than spherical GNPs. We demonstrated that the main parameter in the evaluation of the GNPs toxicity is the GNPs roughness and that this effect is independent on the surface chemistry. We assume that this behavior is highly related to the efficiency of the GNPs internalization within the cells and that this effect is enhanced due to the specific geometry of the flower-shaped GNPs.