Usually, you may have a fever as one of the common side effects of Bacillus Calmette-Guerin strain. But if the fever is prolonged with a temperature of or above 101 degrees, or if you have chills, rash, prolonged cough, specific joint pain, or if any of these symptoms last longer than 48 hours, then you should contact your doctor immediately. Your doctor may prescribe some medications to relieve these side effects and may also suggest ways to cope up with them.