Why do your muscles ache when you have the flu?

Answer 1

There really isn't a solid consensus on this answer. Part of the reason is likely because infection with the flu makes you have hot and cold chills, so you spend part of your day tensed up, shivering and huddled into a ball trying to warm yourself up. Being tensed up like that for extended periods of time makes your muscles hurt because they haven't worked like that in a long time, if ever. Another part of the reason is the cytokine and interleukin proteins that are released - they are part of the inflammatory response that helps your body clear the infection but also makes your body feel feverish and achy.