Combine all of the ingredients in a pan with 3 cups of water. Cover and cook over very low heat for 1 to 1 1/2 hours, until the chilies are very soft and the liquid has been reduced to 1 cup. This recipe will keep for several weeks in the refrigerator in an airtight container. For chipotle puree, place the cooked chipotles and sauce in a blender and puree. Put through a fine sieve to remove seeds. Makes 1 cup.
Chipotles in adobo are chipotles that have been stewed in a lightly seasoned liquid. They have become very popular in Southwestern cooking because the provide a distinctive warm heat and delicious smoky flavor. They can be added to almost anything, including breads, sauces, salad dressings and pastas. Although you can buy canned chipotles in adobo (look for them in markets that specialize in Hispanic foods), this homemade alternative is far superior and is very easy to prepare.