Dentists clinically often face patients with an oral infection. Understanding the microbiota of the oral cavity is helpful to us when managing intra-oral/extra-oral infections and helps with the effective use of antibiotics. Although research has clearly indicated that intra-oral infection may involve certain systemic diseases, the link is still at the stage of association, and no direct evidence of cause and effect has been proved. This article uses evidence-based medicine to identify whether antibiotic prophylaxis is beneficial to individuals at risk of infectious endocarditis and whether the use of antibiotic before or after implant surgery is able to reduce the failure rate of implant surgery. Our aim is to set guidelines for dentists to follow in daily clinical practice and during implant surgery.