Whole Foods Market, the US-based natural and organic retailer, has seen costs linked to its recent acquisition of rival Wild Oats Markets hit full-year profits.

Whole Foods saw operating income fall almost 7% in the 12 months to the end of September.

The retailer said it had paid around $596m for Wild Oats, including $34m in costs linked to the acquisition. Whole Foods won a tense legal battle with the Federal Trade Commission for the right to buy Wild Oats. The US anti-trust body had sought to block the deal on competition grounds.

Nevertheless, Whole Foods was upbeat about its prospects. It said annual sales had risen 5.8% – on an identical store basis – to $6.6bn.

“We are very excited about the progress of our integration of Wild Oats and the healthy increase in sales growth we are seeing at the Wild Oats stores from 3.9% in Q4 to 6.6% quarter to date,” said Whole Foods chairman and CEO John Mackey.

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“We expect these stores, along with our new stores, to drive strong sales this year and strong comparable store sales growth in fiscal year 2009 and beyond.”