The organ of Santiago Comaltepec is distinguished by its excellent state of preservation, striated case painting, and unusually fine upper case carvings. After more than 200 years, only six pipes are missing; the rest of the organ is intact. It is stylistically on the cusp of the baroque and neo-classical periods. A cross on the crest is the only religious decoration. In the late 19th/early 20th century, the original stop action was modified in a rather odd way, combining some ranks and separating others. The façade pipes are light colored and firm due to a high percentage of tin in the alloy. The reed pipes are darker and more malleable and have a higher percentage of lead.