Brown semen may be due to hematospermia. It can occur due to many conditions such as infections, swellings (inflammations), cysts, stones & other obstructive lesions, and benign or non-benign tumors of the organs of the genitourinary system (involving the bladder, urethra, the testicles, the seminal vesicles, the epididymis, the prostate gland etc).
Investigations include blood tests, routine & culture tests of urine & semen, ultrasound & MRI scans of genitourinary system, and histopathological tests (FNAC, biopsy etc). So, I suggest you to consult a General Surgeon for a thorough medical check-up and appropriate tests as you might need treatment (medicines and/or surgical intervention) for management of your condition.
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