Brown semen is frequently from traces of blood which can come from injury, blockage, infection or inflammation anywhere in the reproductive system including the urethra, testicles, epididymis, or prostate. Often inflammation of the seminal vesicles is the problem and it usually clears up without intervention. Sometimes, no reason for the blood is ever found. If you continue to have blood, please see your medical provider doctor for an examination and testing to determine where the blood is coming from. Here is some more information.