Porphyromonas gingivalis peptidylarginine deiminase (PPAD), an isoenzyme of animal endogenous peptidylarginine deaminase, is secreted by the Por system and catalyzes the citrullination of arginine. Recent studies have found that PPAD can affect the formation of Porphyromonas gingivalis biofilm and reduce the body′s immune defense function, which is related to the occurrence and development of many diseases such as periodontal diseases and rheumatoid arthritis. In this paper, we reviewed the molecular characteristics of PPAD, including the genetic and functional characteristics, as well as the mechanisms related to the inflammatory and autoimmune diseases. We also pointed some issues that should be pay attention to in the further study.