Background: The United States Department of Agriculture's (USDA) new nutrition standards for school meals include sweeping changes setting upper limits on calories served and limit milk offerings to low fat or fat-free and, if flavored, only fat-free. Milk processors are lowering the calories in flavored milks. As changes to milk impact school lunch participation and milk consumption, it is important to know the impact of these modifications. Methods: Elementary and middle schools from 17 public school districts that changed from standard flavored milk (160-180?kcal/8?oz) to lower calorie flavored milk (140-150 kcal/8?oz) between 2008 and 2009 were enrolled. Milk shipment and National School Lunch Program (NSLP) participation rates were collected for 3 time periods over 12?months (pre-reformulation, at the time of reformulation, and after reformulation). Linear mixed models were used with adjustments for free/reduced meal eligibility. Results: No changes were seen in shipment of flavored milk or all milk, including unflavored. The NSLP participation rates dropped when lower calorie flavored milk was first offered, but recovered over time. Conclusions: While school children appear to accept lower calorie flavored milk, further monitoring is warranted as most of the flavored milks offered were not fat-free as was required by USDA as of fall 2012.