Researchers from Yale University believe the herpes virus spreads from the genitals to nerves in the spinal cord and then on to the colon, where it kills off neurons.
This damage then prevents the movement of food along the digestive tract, causing constipation.
While the study was done in mice, the study's authors believe the findings could help patients with chronic gastrointestinal diseases with no clear cause.
In the past, individuals with herpes have reported seemingly unrelated symptoms such as constipation and inability to empty the bladder.
To understand why, researchers wanted to investigate the link using mice with the herpes simplex virus-1 (HSV-1), the dominant cause of genital herpes in the US.
According to the World Health Organisation, HSV-1 is mainly transmitted by oral contact such as kissing or oral sex.
The damage to the colonic neurons prevented the movement of food along the digestive tract, leading to an enlarged colon and disease.
While the effects in mice are distinct from what happens in people with herpes, the study reveals a previously unrecognised disease process.
"The key finding is that there is this unexpected infection in the neurons in the colon wall after herpes infection," said Akiko Iwasaki, lead author and professor of Immunobiology.
"Other members of the herpes virus family, including Epstein-Barr virus, chicken pox virus, and cytomegalovirus have been found in the neurons of the colon of people with unexplained chronic constipation.
"When doctors can’t figure out the cause of these chronic intestinal conditions, one thing to look at is a viral infection."
The findings were published in the journal Cell Host & Microbe.