Multicellular creatures consist of a symbiosis between the host and its colonizing bacteria. The oral cavity may contain as many as 19,000 bacterial phylotypes, while each individual presents a proportion of these microbes. Infectogenomics studies the interaction between host genetic variations and composition of the microbiota. This review introduces the concept of periodontal infectogenomics, defined as the relationship between host genetic factors and the composition of the subgingival microbiota. In particular, the evidence for the effect of genetic variants in neutrophil and cytokine genes and the presence of periodontopathogenic bacteria will be discussed. The influence of genetic factors may affect clearance or persistence of pathogenic bacteria subgingivally, therefore increasing the risk for the development of common pathogenic conditions such as gingivitis and periodontitis, leading to early tooth loss. Mechanisms of interaction between genetic and microbiological factors and prospects for future studies will be discussed.