His Dimension Data team said the 33-year-old British cyclist will take a break from the sport after finding out the 2011 world road race champion had been training with EBV without realising it over the past few months.
Cavendish said: "Despite showing good numbers on the bike I have felt that there's been something not right.
"I'm glad to now finally have some clarity as to why I haven't been able to perform at my optimum level during this time."
Here are the answers to key questions about the infection.
- What is Epstein-Barr virus?
The Epstein-Barr virus (EBV) is one of the most common human viruses. It is part of the herpes virus family.
Most people become infected with EBV at some point in their lives.
- What are the symptoms?
Symptoms can include fatigue, fever, rash, swollen lymph nodes in the neck or an inflamed throat, a swollen liver and an enlarged spleen.
Many people become infected in childhood, with such infections either causing no symptoms at all, or very mild symptoms.
Those who do contract the virus and develop symptoms, usually teenagers or adults, usually get better in two to four weeks, though some may feel fatigued for months.
After someone becomes infected, the virus stays latent in their body and in some cases it may reactivate.
- How do people contract the virus?
Transmission most commonly occurs through bodily fluids, primarily saliva.
This can occur through kissing, sharing drinks and food, using the same cups, eating utensils, or toothbrushes, or having contact with toys that children have dribbled on.
However, the virus can also spread through blood and semen during sexual contact, blood transfusions, and organ transplants.
- How can it be diagnosed?
The virus can be detected through a blood test which detects antibodies.
- What is the treatment?
There is no specific treatment for the virus but people can take steps to relieve symptoms including rest, staying hydrated and taking over-the-counter medicines for pain and fever.
- Is it linked to any other illness?
EBV can cause infectious mononucleosis, more commonly known as glandular fever, as well as other illnesses.
Those with a weakened immune system may develop more serious symptoms and complications from the virus, they may also have a more severe illness caused by the infection.
EBV can affect a person's brain spinal cord ad nerves and cause conditions including viral meningitis, encephalitis.
It can also affect a person's blood and bone marrow and has been linked to some cancers including cancer of the lymphatic system and cancer of the upper throat.
It can also cause pneumonia, pancreatitis or swelling of the heart muscle.