Herein, a library of gold nanorods (GNR) decorated with polyethylene glycol-thiol (PEG-SH) containing different functionalities were synthesized and characterized by optical absorption spectroscopy, zeta potential, dynamic light scattering (DLS), transmission electron microscope (TEM) and proton nuclear magnetic resonance (
1
H-NMR). The colloidal stability of GNR when exposed to skin, and their preferential accumulation into excised human skin layers were investigated. Confocal laser scanning microscopy, transmission electron microscope (TEM) and inductively coupled plasma-optical emission spectroscopy (ICP-OES) were utilized to track the penetration of GNR into different skin layers. The results demonstrated that cholesterol-PEG coated GNR were preferentially loaded up in the upper layers of skin (stratum corneum), while phospholipid-PEG coated counterparts were drastically deposited in skin dermis. Neutral methoxy-PEG-coated GNR were distributed in both SC and dermis skin layers, while charged GNR (anionic-carboxylic acid-PEG-GNR and cationic-amine-PEG-GNR) revealed a minimal accumulation into skin. DSPE-PEG-GNR and Chol-PEG-GNR demonstrated antibacterial activities against
Staphylococcus aureus
(
S aureus
) at MIC values of 0.011 nM and 0.75 nM, respectively. Photothermal treatment for
S. aureus
at sub-MIC concentrations resulted in a significant bactericidal effect when using Chol-PEG-GNR but not DSPE-PEG-GNR. Gold-based nanoscale systems have great value as a promising platform for skin diseases therapy.