American children are overweight and undernourished. It is critical that school meals provide foods that help children achieve a healthy, balanced diet, and in recent years, some schools have removed flavored milk. The primary goal of this study was to quantify the impact of changes in flavored milk availability on school children’s milk consumption. A secondary goal was to explore potential implications on nutrient intakes at school meals and cost to schools as a result of changes in milk consumption. Measurements of milk sold and the cumulative ounces of milk discarded at school breakfast and lunch were recorded on an average of 12 observation days at 49 elementary schools that had changed flavored milk availability over the past 2 years. When flavored milk was removed on 1 to all days of the week, there was a 26.0% reduction in milk sales and an 11.4% increase in the percentage of milk discarded, resulting in a 37.4% decrease in milk consumption. The Jefferson County school district in Colorado was further evaluated to determine what foods could hypothetically replace the nutrient deficit from lower milk consumption without adding extra calories, fat, or sugar. Alternate foods commonly served at the schools were selected, and the nutrient changes were examined using the US Department of Agriculture National Nutrient Database. The resulting changes in cost were also determined using actual food prices from this school district. It would require 3 to 4 additional foods, resulting in more calories and fat, to replace the nutrient deficit from this decline in milk consumption, a cost increase of up to $4600 more per 100 students per year in their district. Removing flavored milk from schools had significant unintended consequences on children’s milk consumption, which could negatively impact nutrient intake and should be further evaluated.