The company said sales at locations open at least a year increased 2.6 percent for the month. Sales at stores open at least one year is considered a key measurement of retailer health because it excludes results from stores that opened or closed over the last 12 months. Thomson Reuters says analysts were expecting those sales to rise 4.9 percent.

Walgreen said pharmacy revenue from stores open at least a year rose 3.1 percent and revenue from "front-end" sales of items like cosmetics increased 1.7 percent. Both fell short of analyst estimates. Prescriptions filled at those stores increased 2.5 percent. The company said it believes its impending split with Express Scripts reduced prescriptions by 0.6 percent.

Express Scripts, one of the largest pharmacy benefits managers in the U.S., pays Walgreen and other drugstores to fill prescriptions. A three-year contract between the companies expires at the end of 2011, and they have been unable to come to terms on a new deal. Express Scripts recently said the companies are not negotiating and Walgreen said Thursday that it is assuming it will not be part of most of Express Scripts' pharmacy networks in 2012.