ABSTRACT: Viral diagnostic tests are categorized as direct diagnosis, indirect examination (virus isolation), and serology. Molecular testing is often done to detect potent viral markers resulting from any gene or chromosomal modifications during viral replication in the host. The clinical specimen is tested specifically in direct analysis for the presence of virus particles, virus antigens or viral nucleic acids. Molecular diagnosis of viruses can be achieved from clinical samples like blood, hair, skin, amniotic fluid, or other tissue. Molecular biology techniques are considered to be the standard and confirmatory protocols in the analysis of viral DNA, RNA and protein. Molecular viral diagnosis are considered to be more specific and sensitive in preliminary viral screening and can pave the way for rapid diagnosis. However, the procedures are costly and involve automated bio-instruments to perform the same. This review thus highlights the various molecular diagnostic methods used in diagnostic virology with their limitations and challenges.