Infectious diseases, which pose a great threat worldwide, have a significant impact on public health and the world economy. It contributes to increased healthcare costs, unnecessary drug-related side effects, and increased antimicrobial resistance. It is not always easy to distinguish the etiological differentiation of diseases that can develop with bacteria and viruses. Therefore, one of the biggest challenges in medicine is how to correctly distinguish between the different causes of these infections and how to manage the patient. Because bacterial and viral infections often present similar symptoms. The real decision is whether the infection is caused by bacteria or viruses and whether to treat the patient with antibiotics. There are many different methodological approaches to diagnosing infections. Biomarkers have been used in the diagnosis of diseases and other conditions for many years. Biomarkers are molecules found in blood and body fluids in measurable amounts, which can evaluate biological and pathological processes. These key indicators can provide vital information in determining disease prognosis, predicting response to treatments, adverse events and drug interactions, and identifying key risks. An effective biomarker is extremely important for the early diagnosis of various diseases. The explosion of interest in biomarker research is driving the development of new predictive, diagnostic, and prognostic products in modern medical practice. The purpose of this review is to demonstrate the use and diagnostic potential of current and investigational biomarkers in the distinction between bacterial and viral infections.