Step 1Remove the seeds and stems from the chipotle, ancho and guajillo chiles. Place the chiles, onion and garlic in a large saucepan and cover with plenty of water. Bring to a boil, reduce the heat and simmer 15 minutes.
Step 2With a slotted spoon, transfer the chiles, onion and garlic to a food processor, reserving the liquid. Add the brown sugar, cumin, oregano, tomato paste and 1 cup of the reserved chile liquid. Puree, adding more of the chile liquid until the ketchup reaches the desired thickness. Add salt and pepper to taste. Tightly sealed in a glass jar, the ketchup will keep refrigerated for several months.