Microorganisms refer to invisible entities such as viruses, bacteria, fungi, and protozoa that have various structures and characteristics. These entities exist not only in the factors that humans come into contact with, such as soil, water, and air, but also on and inside humans. These living things have very different vital activities, and some of them can be pathogenic for humans. Human brain health can be negatively affected directly or indirectly by pathogenic microorganisms. In this book chapter, scientific studies on pathogenic microorganisms that have a negative impact on human brain health are included. Additionally, scientific studies on the microbiota-host context, which affects brain health, are also included in the context of brain health-pathogenic microorganism. It is anticipated that the current study, which was prepared in the form of a review, will contribute to those interested in the subject.