Chocolate contains oxalate — a naturally occurring compound in cocoa beans — which can inhibit the absorption of calcium. Calcium binds to oxalate in your intestines, limiting its absorption into your bloodstream. People with oxalate kidney stones, which could occur when there is too much oxalate in the urine, should limit the amount of oxalate in their diets.
The jury is still out, however, on whether chocolate causes problems for healthy people who eat calcium-rich diets. A 2008 study suggests there might be reason for concern. The study found that elderly women who ate one or more servings of chocolate a day had lower bone density and strength than did women who ate fewer servings of chocolate. Researchers believe this may be due to oxalate inhibiting calcium absorption — but it could also be due to the chocolate's sugar content, which may increase calcium excretion. In addition, chocolate also contains flavonoids, which are thought to be beneficial to health. Further research is needed to fully determine the role chocolate plays in calcium balance and bone strength.
In the meantime, if you get the daily recommended amounts of calcium and vitamin D from food or supplements, and practice weight-bearing exercise, eating chocolate in moderation is unlikely to adversely affect your bone health.
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