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Nearly 13 million customers signed up for Walgreen Co.’s new Balance Rewards loyalty program in September, though the Deerfield-based drugstore chain continued to struggle with decreased sales in the month.

Balance Rewards, launched Sept. 16, marked a major marketing initiative for the company, which had resisted putting such a program in place despite well-established offerings from rivals such as CVS Caremark Corp. and Rite Aid Corp.

Walgreens said comparable store sales fell 11.1 percent in September from the same month last year. The company attributed the decline to unfavorable calendar shifts and the introduction of generic drugs, a development that hurt pharmacy sales. Comparable store front-end sales dropped 1.5 percent, as a reduction in customer traffic offset a small uptick in purchase size.

The year-on-year drop was felt mostly in the pharmacy department, where prescriptions filled at fell 10.3 percent on a comparable store basis. Walgreens noted that September 2012 had one additional Saturday and Sunday and one fewer Thursday and Friday than the year-earlier month; this calendar change cost the drugstore 3.5 percentage points. Comparable store pharmacy sales tumbled 16.1 percent.

The company also noted that it has administered nearly 1.5 million flu shots this season, down from 1.8 million in the period last year.

For the calendar year, Walgreens’ sales totaled $51.96 billion, down 3.8 percent from 2011.