Body aches are a symptom that often accompanies the cold or flu. The common cold and the flu are both illnesses that affect the upper respiratory system and have similar symptoms but are caused by different viruses. The easiest way to tell the difference is by looking at the severity of the symptoms; cold symptoms are usually milder than flu symptoms.4 While it can seem like body aches are a part of the virus itself, they’re actually caused by your immune system’s response to it. As your body works to fight the virus, it can cause body aches and inflammation all over.2 While our bodies are launching an attack against the infected cells, the immune cells that are fighting the flu release a protein that can cause inflammation and body aches.2