Chipotle peppers are basically ripened jalapeño chiles that have been smoked and dried. They can be ground and used in many Mexican and Tex Mex cooking and are typically sold in a rich, smokey flavored adobo sauce.
For the wood chips or pellets, pecan is the traditional Mexican wood, but I also like to use a mild, fruity wood like apple or cherry. Hickory or oak work well too if you don't have the others. We will be smoking for 3 hours, so plan accordingly.
Wash and dry the jalapeños. Make a slit with a paring knife from stem to tip along the side of each chile pepper. Place in a single layer on a wire rack (or racks) that will fit the inside of your smoker.
Smoke the jalapeños for 3 hours. Remove from smoker (and if not storing in adobo sauce) you will need to dry these completely, see below step.
Using a dehydrator works best (125-135°F), but 10+ hours in an oven set at its lowest temperature, or 170-200°F depending on your oven (convection), will do (See Note 1). Store in an airtight container or grind for chipotle powder.
Notes
I typically use 6 inch or larger jalapeños. If you can find red, all the better, or allow to ripen and turn red. If drying in oven, any jalapeños smaller than 6 inches in size you will dry in 4-6 hours, depending on oven and thickness of jalapeños. If 6 inches or larger, drying time is 6-10 hours, depending on size and thickness. Use you discretion in timing as ovens vary. I have also used my convection oven set at 170-200°F and dried 6 inch jalapeños in 6-7 hours as well. Length of time depends on type of oven and thickness of jalapeños.
If you want to store the smoked peppers in adobo sauce... I take them straight from the smoker and add the freshly smoked peppers directly to the adobo sauce, skipping the other 10 hour drying process. Simmer for another 20 minutes. Let cool completely and store all in an airtight container in the refrigerator. To learn How to Make Adobo Sauce, see this recipe.