The most common side effects with Cialis are headache, indigestion, back pain, muscle aches, flushing, and stuffy or runny nose. These side effects usually go away after a few hours. Patients who get back pain and muscle aches usually get it 12 to 24 hours after taking Cialis. Back pain and muscle aches usually go away by themselves within 48 hours. Call your doctor if you get a side effect that bothers you or one that will not go away.