What is behind muscle pain and stiffness? Is it a cytokine thing, or is one of our common pathogens particularly likely to cause muscle aches? My very sudden onset illness was remarkable for the degree of muscle aches and stiffness (and cognitive dysfunction). Now, even though the pain is ordinarily under control, the first thing that shows up with PEM/PENE is muscle aches and stiffness. My joints pop when I rotate them and I become clumsy and stiff. It's like flu-like muscle aches, but worse. If I had a clue as to what's at the root of this symptom, I might be able to moderate it if I know I have to overdo. Any ideas?