When comparing the nutrient values of the different green peppers, studies have shown that red peppers have significantly higher levels of nutrients than green. Red peppers also contain lycopene, which is a carotene that helps to protect against cancer and heart disease.

Possibly due to their vitamin C and beta carotene content, green peppers have been shown to be protective against cataracts. Just like other nutrient-dense vegetables, green peppers contain many different powerful phytochemicals. Green peppers have also been shown to prevent blood clot formation and reduce the risk of heart attacks and strokes probably due to their content of substances such as vitamin C, capsaicin, and flavonoids. Although chili peppers contain a higher amount of those substances, green peppers should still be promoted especially for individuals with elevated cholesterol levels.

Source: http://www.everynutrient.com/healthbenefitsofbellpeppers.html