Heavy use of chilies may increase the risk of stomach cancer. This appears to be the major stumbling block when it come to the health effect of chillies. Opinion seems to vary greatly as to whether chillies help prevent or cause stomach cancer. Researchers at Yale University of Medicine concluded in 1994 that chili pepper consumption may cause increased risk of stomach cancer.
Another recent study by Mexico National Institute of Public Health found higher rates of gastric cancer in people with high chillie intake (9-25 jalapenos a day!). However no clinical evidence was found that it was the chillies that were causing the increase in cancer.
A Berkley neurobiology study however found the opposite to be true. They concluded that capsaicin/chillie consumption to be "protective against stomach cancer".
Perhaps rather predictably there is no clear answer to the question 'are chillies good for you?'. However there is mounting evidence that chilies may do more good than harm.
My advice would be to stop worrying and start cooking!
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