In this book, we introduce a new concept in the field of human microbiota in health and disease. The fundamental idea is that both fungi and bacteria can be found in some internal tissues that should be "sterile", which can lead to polymicrobial infections. In the absence of symptoms, these infections may go unnoticed over many years or decades. However, if the number of fungi and/or bacteria in a given tissue increases due to, for example, stress, changes in diet, lifestyle, etc., clinical symptoms may begin to emerge, which can vary greatly depending on the affected tissue. This diversity in symptoms will also depend on the specific species of fungi and/or bacteria that affect each individual. The internal microbiota may be the root cause of numerous diseases in humans whose etiology is still unknown. Among these diseases, we can include neurodegenerative, cardiovascular, ophthalmological, rheumatic and allergic diseases, among others. This concept has been studied and published in many different scientific works of our research group in recent years. We have determined the species of fungi and bacteria that can exist in the nervous system – mainly in the brain of patients with different neurodegenerative diseases (NGDs) such as Alzheimer's, Parkinson's and Huntington's disease, amyotrophic lateral sclerosis (ALS) and multiple sclerosis. In this book, I first present an overview of this concept and I then indicate the potential possibilities for proper diagnosis and more appropriate treatments for these human diseases whose cause remains unknown. The treatment of polymicrobial infections in internal tissues is very complex and it will take some years to determine the most appropriate therapeutic strategy to combat them. At the moment, it is more about laying the foundations to determine the etiology of these diseases and initiating new lines of research aimed at elucidating the most effective therapeutic options.