Combine all of the ingredients in a medium saucepan. Bring to a boil, reduce to a simmer and cook, uncovered, about 20 minutes. The liquid should be reduced by one-third and the tomato skins should be falling off. Set aside to cool.
Pour the mixture into a blender or a food processor fitted with the metal blade. Puree until smooth and then pass through a strainer. Serve chilled. Chipotle salsa can be stored in the refrigerator up to 5 days or frozen.
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