The soldier was shot up to five times November 13 while making a run for the South Korean side of the border through the heavily fortified Demilitarized Zone, according to dramatic security video released this week.
The defector, whose last name is Oh, required emergency treatment for his wounds, including extensive surgery. Doctors discovered a large number and multiple forms of parasitic worms.
Some of the parasites removed were as long as 27 centimeters (more than 10 inches), according to the South Korean doctors who treated him. One type of worm they discovered is typically found in dogs.
"In my 20 years as a surgeon, I have only seen something like this in a medical textbook," Lee Cook-Jong, the man's surgeon, told reporters on November 15.
David Heymann, professor of infectious disease epidemiology at the London School of Hygiene and Tropical Medicine, told CNN that the transmission of hepatitis B was usually a good indication of a country's poor sterilization practices in hospitals.
"Hepatitis B is mainly transmitted either through unsterilized needles or syringes ... or by sexual activity," he said.
It isn't the first time a North Korean defector has been found to have large numbers of stomach parasites or hepatitis B.
One in ten of the total subjects were also discovered to have hepatitis B.
Choi Min-ho, a professor at Seoul National University College of Medicine who specializes in parasites, told CNN the use of human fertilizer on crops and poor sanitary conditions led to the transmission of parasitic cysts in North Korea.
Intestinal worms are typically transmitted through contact with feces or unwashed hands. Infections are easily treated with drugs.
"It is a vicious cycle that is hard to stop in North Korea. They are so desperate to make ends meet that they cannot take proper preventive measures," he said.
Choi said he believed at least half of North Korea's population were likely to have parasites. "For those who can eat well and are healthy, parasitic infections might not be a big deal. But for those malnourished, this can be much more critical as parasites steal much-needed nutrition."
Meanwhile, the UN World's Food Programme estimates as much as 70% of the country's 25 million people still don't eat a "sufficiently diverse diet."
Doctors described the soldier's condition now as great, with Lee saying all parasites had been removed from his system.
CNN's Jake Kwon contributed to this report.