Many efforts have been devoted to developing functional poly(ethylene terephthalate) (PET) due to its special biomedical applications in surgical meshes, heart valves, vascular grafts, artificial ligaments, etc. However, for antimicrobial PET the release of antimicrobial component remains a concern. In this work, an antimicrobial compound with terminal epoxy group was synthesized by ethylene glycol diglycidyl ether (EGDE) and polyhexamethylene guanidine hydrochloride (PHMG). Then, EGDE-PHMG was chemically bonded with PET surface through a reaction between the epoxy group of EGDE-PHMG and the amino group of aminated PET to generate non-leaching and permanent antimicrobial PET. The content of PHMG on PET surface, morphology and hydrophilicity of surface, antimicrobial activity and mechanical property of PET were investigated. The amount of EGDE-PHMG on PET surface reached at 3.96nmol/cm(2), resulting in excellent antimicrobial activities against Escherichia coli and Staphylococcus aureus with above 99.99% of inhibition rates. Due to the good hydrophilicity, excellent antimicrobial property, non-leaching characteristic of antimicrobial component and good mechanical properties, the as-prepared antimicrobial PET was promising in the biomedical applications.