Humanity has suffered from many epidemiological diseases and pandemics throughout history. The course of many diseases has changed thanks to the possibility of knowing who is causing them. Microscopy has been a fundamental tool in the clinical and research findings of the etiological agents of several diseases, allowing a correct diagnosis to be made. There is no other tool that allows us to observe the tiny etiological agents, from those that cause bacterial infections to those that cause viral pandemics, but microscopes are also very necessary in clinical life; they are used daily to review vaginal exfoliative cytology (pap smear) tests or to review urine samples from patients with kidney problems. In this chapter we will describe some of the most used techniques to detect causative agents with different approaches from light microscopy and electron microscopy.