Causative agents of sexually transmitted diseases (STD) are different types of bacteria, viruses, fungi and protozoa. The last two decades of the twentieth century were marked with a sudden rise in the number of cases of STDs. Human immunodeficiency virus (HIV), which emerged in the 1980s, is the most prominent STD agent because of its fast spread and severity of the disease it causes, acquired immunodeficiency syndrome (AIDS). Beside HIV, human papillomaviruses (HPVs), herpes simplex viruses (HSVs) and Chlamydia trachomatis are nowadays among most health-threatening STD pathogens. In order to stop the spread of infection, apart from education about precautions, early detection of the disease is essential. Although most STD pathogens can be detected by classical methods of cultivation, biochemical and/or serologic methods, molecular diagnosis of infectious diseases has largely simplified and accelerated their detection. For instance, HPVs that cause benign and malignant tumors of genital skin and mucosa cannot be routinely detected on cell culture, whereas serologic analysis is not sensitive and informative enough. Moreover, cytologic (Pap smear) and histologic analyses can indicate changes associated with HPV infection, but neither of these methods can prove the presence of HPV. That is why the molecular methods are essential to demonstrate the presence of the infection and, even more important, to determine the type of the virus, which is associated either with low-grade or high-grade genital lesions. There are numerous methods based on hybridization with DNA or RNA probes, some of them are suitable for detecting wide range of types and screening of large collection of samples. However, the most sensitive and informative methods are based on polymerase chain reaction (PCR), and they have the advantage of being able to determine the type of the virus and distinguishing between multiple infections. Herein, we present when and why molecular analysis is useful and necessary for the detection of STD agents.