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Green jalapenos are great, especially in pico de gallo and other salsas, when you can't wait for red ones, but they don't have the deep flavor and sweetness necessary for the quintessential chipotle. Some farmers' markets sell red jalapenos, or you can make a special request to a grower, as a friend did, to let the peppers ripen before picking. Best yet is to grow them yourself. If you have a climate comparable to the Rogue Valley (or Southern New Mexico), no problem!
PK is a pepper addict whose passion I've come by through osmosis. I use chipotle —and about a dozen other peppers—year-round in my own kitchen, and love giving chipotle peppers as a special gift to friends and family. Here's what a smoker load of about-to-be chipotle peppers looks like. The stems are removed, but that's it for prep. So pretty!
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Once the peppers come out of the smoker, they are anywhere from brittle to slightly pliable. If they're still tacky, they should be stored in the freezer. I put most in glass jars. This year, the first batch wasn't out of the smoker for 10 seconds—we had a pent-up demand for chipotle, nerves were frayed—before I snared enough to stuff a pint jar, fill it with scalding water, and wait a few hours for those babies to rehydrate so I could make chipotle cubes.