Human interaction with natural ecosystems, such as deforestation and animal markets, increases the risk of the emergence of new zoonotic viruses. Added to this is the constant mutation of already existing viruses, such as influenza, which can trigger new epidemics. Additionally, climate change alters animal migration patterns, thus facilitating the spread of infectious diseases. Among the recent outbreaks of viral respiratory diseases, the most notable are COVID-19 (SARS-CoV-2), which emerged in 2019 in Wuhan, China; the H1N1 swine influenza pandemic, which appeared in 2009 in Mexico; and avian flu, caused by the AH5N1 and AH7N9 influenza viruses, recorded since 1997 with limited transmission from birds to humans. Other outbreaks include AH3N2 and AH5N6, which have emerged since 2016, causing isolated cases with symptoms like seasonal influenza. Furthermore, within the other coronavirus family, notable mentions include MERS, which appeared in 2012 in Saudi Arabia, and SARS, which emerged in 2002 in China. In general, these respiratory diseases share similar symptoms, ranging from fever and cough to severe pneumonia, making their diagnosis and epidemiological monitoring challenging. For this reason, this chapter will thoroughly address the molecular diagnosis of respiratory diseases as a key tool for the identification and clinical management of these infections.