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Yellow semen completely not a pathological condition but if your semen in deep yellow with foul smelling represent infection.
Yellow color due to neutrophils in the semen.
Causes of yellow semen
Urine in the semen: Semen travels through the same tube of urine travel it may give yellow tinge.
Jaundice:Jaundice most commonly causes yellowing of the eyes but can cause the skin and the semen to appear yellow too.
Abnormally high white blood cells: Inflammation can produce excess white blood cells. These can be released via the semen, a condition known as pyospermia or leukocytospermia.
STIs: A sexually transmitted infection, such as chlamydia,
herpes, or
gonorrhea may cause yellow semen. In this condition semen have unpleasant smell also.
Dietary changes: Eating foods that contain dyes can cause yellow semen.
Some foods such as garlic, onions, asparagus, or broccoli gives smell to semen.
Infrequent ejaculation: If a man has not ejaculated in some time; the semen is more likely to have mixed with urine.
Please consult your doctor he will examine and treat you accordingly.