Generally, the most common cause of epididymitis is bacterial infection, often originating in urine, the prostate, or the ejaculatory duct.
Tuberculosis:
 Mycobacterium tuberculosis can present itself as epididymitis. 
Tuberculosis is a chronic infection of the lungs caused by the 
mycobacterium tuberculosis. The disease is spread through airborne 
droplets expelled from an infected individual’s mouth through coughing, 
sneezing, or spitting. Although it has become increasingly associated 
with immune suppression in AIDS-infected men, this form of epididymitis 
is more commonly found in areas where tuberculosis is still a public 
health problem.
Vasectomy: Vasectomy
 is a surgical procedure for male sterilization and permanent birth 
control. During the procedure, the male vasa deferentia are severed and 
then sealed in a manner so as to prevent sperm from entering into the 
seminal stream and thereby prevent fertilization from occurring. Chronic
 scrotal pain is the most common post-vasectomy complication. Other 
causes of the pain include congestive epididymitis, pain from the nerve 
ending at the incision.
Certain medications 
like heart rhythm drug amiodarone can cause epididymitis. Amiodarone is 
an antiarrhythmic agent used for various types of cardiac dysrhythmias, 
and ventricular andatrial. Amiodarone is sometimes responsible for 
epididymitis, a condition of the scrotum normally associated with 
bacterial infections but which can also occur as a non-bacterial 
inflammatory condition. Amiodarone accumulates in the head of the organ 
and can cause unilateral or bilateral inflammation.
Certain
 diseases like Behcet’s disease also can cause epididymitis. Behcet’s 
disease is a rare immune-mediated small-vessel system that often 
presents with mucous membrane ulceration and ocular problems. It is an 
autoimmune condition that can cause to develop mouth and genital sores 
along with other symptoms. Behçet’s disease can cause male infertility,
 either as a result of the condition itself or of a side effect of 
concomitant medication such as colchicine, which is known to lower sperm
 count.