Calcified nanoparticles (CNPs), also known as nanobacteria, are ubiquitously present in both natural minerals and biological systems. However, their properties remain incompletely elucidated, particularly concerning whether they represent the smallest self-replicating entities on Earth, a topic that remains highly debated. Current research has demonstrated that CNPs can be isolated from various pathological calcification conditions, including kidney stones, vascular calcification, biliary stones, and calculus oral disease. These particles have the potential to infect any tissue or cell type within the human body, forming a mineralized layer around them, which leads to pathological calcification of tissues. It is suggested that CNPs may play a significant role in these diseases by damaging cells, promoting osteogenic differentiation, and influencing metabolic processes, thereby initiating the formation of calcification cores in local tissues. Under the influence of inflammatory responses, these cores can expand further, ultimately leading to the development of calcification diseases. Therefore, the aim of the present review was to explore the roles and pathogenic mechanisms of CNPs in various pathological calcification diseases, providing new insights for in-depth research into their properties and pathogenic mechanisms, as well as identifying potential therapeutic targets for calcification diseases.