A problem addressed by this invention is to provide a medical antimicrobial composition comprising a siloxanyl structure-containing polymer and an ammonium group-containing polymer, which is excellent in transparency, flexibility and mechanical properties, and also excellent in adhesion to a base resin with good mechanical properties, particularly to a silicone resin. Another problem addressed by this invention is to obtain a medical device comprising said medical antimicrobial composition. This invention provides a medical antimicrobial composition in which an ammonium group-containing polymer compound (A) is dispersed in a siloxanyl structure-containing polymer (B).