The National Dairy Council stated in their article "Flavored Milk in Perspective," published on their website (Mar. 12, 2007):

“Flavored milks are as nutritious as unflavored milks. Both types of milk are nutrient dense foods containing a high proportion of essential nutrients in relation to their energy content. Chocolate milk, for example, provides the same essential nutrients as white milk, including calcium, protein, vitamin D, vitamin A, vitamin B12, potassium, phosphorus, riboflavin, and niacin. Like unflavored milks, all versions of flavored milks provide 300mg calcium per serving or about one-third to one-fourth of children’s daily calcium recommendation.

The main difference between flavored milk such as chocolate and unflavored milk is the 2 to 4 teaspoons more sugar (sucrose or high fructose corn syrup)… Intake of sugar may contribute to dental caries [tooth decay], but it is unlikely that flavored milks cause this disease. Flavored milks, being liquid, do not readily adhere to tooth surfaces. Also, components in flavored milks may protect against dental caries…

The minute amount of caffeine in chocolate milk, which is similar to the amount in decaffeinated coffee, is generally considered too small to affect most children’s behavior or health.”

Mar. 12, 2007