Traditional reporting by physicians recorded only 31 such complications, the study authors noted.
Almost half of the visits were due to abdominal pain, 12 percent to gastrointestinal tract bleeding and 11 percent involved chest pain, the researchers found.
Older patients were more likely to have complications.
Although most of the complications were minor, the cost of follow-up care was not. The average cost per emergency room visit following endoscopy was $1,403 and the average cost of hospitalization for post-procedure complications was $10,123, the researchers reported.
The findings may help guide how doctors counsel patients following one of these procedures.
"We've done a lot over the years to mitigate the risks of bleeding and perforation, and rightly so," Leffler said. "Now [that] we know of the underlying iceberg of minor complications, we can really look at those because they're a significant burden to patients and the health-care system. Most of these patients go home at the end of the day," he noted.
"We can alert patients that [certain symptoms] are common and here are some things you can try -- heating pads, things like that," he said. "If it's persistent and there are certain warning signs, they should let us know."
Leffler also pointed out that electronic medical records might emerge as a more rigorous way to determine complications from different hospital procedures.
Dr. Vivek Kaul, acting chief of the division of gastroenterology & hepatology at the University of Rochester Medical Center, said he was not particularly surprised by the findings.
"These types of events are not uncommon," he said. And "symptoms should be triaged [for example, first by a phone call to a doctor] before people are directed to the ER unless the symptoms are catastrophic. I don't think you can not direct patients to call or go to the E
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