The majority of chronic infections are associated with mono- or polymicrobial biofilms, having a significant impact on the patients’ quality of life and survival rates. Although the use of medical devices revolutionized health care services and significantly improved patient outcomes, it also led to complications associated with biofilms and to the emergence of multidrug resistant bacteria. Immunocompromised patients, institutionalized or hospitalized individuals, elderly people are at greater risk due to life-threatening septic complications, but immunocompetent individuals with predisposing genetic or acquired diseases can also be affected, almost any body part being able to shelter persistent biofilms. Moreover, chronic biofilm-related infections can lead to the occurrence of systemic diseases, as in the case of chronic periodontitis, linked to atherosclerosis, cardiovascular disease and diabetes. The more researchers discover, new unknown issues add up to the complexity of biofilm infections, in which microbial species establish relationships of cooperation and competition, and elaborate phenotypic differentiation into functional, adapted communities. Their interaction with the host’s immune system or with therapeutic agents contributes to the complex puzzle that still misses a lot of pieces. In this comprehensive review we aimed to highlight the microbial composition, developmental stages, architecture and properties of medical biofilms, as well as the diagnostic tools used in the management of biofilm related infections. Also, we present recently acquired knowledge on the etiopathogenesis, diagnosis and treatment of four chronic diseases associated with biofilm development in tissues (chronic periodontitis, chronic lung infection in cystic fibrosis, chronic wounds) and artificial substrata (medical devices-related infections).