The sol-gel method was employed to synthesize hydroxyapatite (HAp) coatings modified with Ag or Zn ions onto Ti-6Al-4V substrate. A bacterial strain Streptococcus mutans (S. mutans) and a human gingival fibroblast (HGF-1) cell line were used to investigate the antimicrobial effect and biocompatibility, respectively. HAp coatings containing 100 ppm Ag(+) ions suppressed the growth of S. mutans. An apparent inhibition zone around the HAp coating was further observed at Ag(+) concentration up to 10,000 ppm. However, for coatings containing Zn(2+) ions, a clear inhibition zone was observed at Zn(2+) concentration of 10,000 ppm. Nevertheless, the results of HGF-1 cultivation demonstrated that the Zn(2+)-modified HAp coatings exhibited better attachment and spread of HGF-1 than did the Ag(+)-modified coatings. Zn(2+) modified HAp coatings also increased the plating efficiency of HGF-1 cells. The cytotoxicity associated with the addition of Ag and the cell-conductive capacity associated with the addition of Zn are proportional to the added concentration, from 100 to 10,000 ppm. The dosages of both Ag(+) and Zn(2+) ions that should be added to HAp coatings were considered to prevent infection and improve biocompatibility. The results of this study ensure that HAp coatings modified with a moderate amount of Ag/Zn efficiently resist microorganisms and improve biocompatibility.