Regulators say they have received more than 30 reports of liver damage in patients taking alli and Xenical, the prescription version of the drug.
Twenty-seven patients had to be hospitalized, and six suffered liver failure.
Only 2 of the liver damage cases were in the United States.
The FDA approved Alli for over-the-counter sale in 2007. Xenical has been available by prescription since 1999. Alli has half the dose of the active drug that Xenical has.
Both marketed by British drugmaker GlaxoSmithKline, though Xenical is manufactured by Swiss firm Roche.
The FDA says it has not established a definitive relationship between the weight loss drugs and liver injury.
The agency says patients should continue using the drugs as directed. And doctors should not change their prescribing practices for Xenical.
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