Short-coats and long-coats both vary in length, texture and thickness, but feathering on the tail, legs, and behind ears is distinctive of the long-coat variety. Long-coat is inherited as a recessive to short-coat. Although it is considered fully recessive, there are hints as to whether or not a short-coat Chihuahua carries a hidden copy of the long-coat trait.

Long-coat Chihuahuas have finer, longer hair that is often silky and often rather thick and stand-offish. At birth, long-hairs do not have significantly longer hair, except on the face in front of the inside corners of the eyes, and often on the bottoms of the feet. However, the hair is noticeably finer in long-haired newborns, visibly silky on the face, and tends to waviness when wet. The coat of a long-coat will continue to grow for 1-2 years. Spayed & neutered long-coat chihuahuas will have a fuller, longer coat, so if the dog is neutered older than 1-2 years, the coat will again improve at that time.

An unnamed "shedding" gene is responsible for about half of the variation in coat thickness: one variant has a moderately thick double coat, noticeably thicker in winter than summer, with a tendency towards an annual shedding in late spring or early summer. The other variant has almost a single coat, with a finer outercoat and very minimal undercoat, leading to much less tolerance to the cold. Intermediate dogs carrying both variants more closely resemble the single coat. Under good conditions, all chihuahuas fall within the classification of low shedding. Given a poor diet, poor lighting, health problems, or high stress, all will shed heavily. In show dogs, double coats are more desirable in long-coat chihuahuas, because it causes the coat to stand off from the body; and smooth single coats are more desirable in short-coats. Some pet owners, however, prefer the reduced shedding of the single-coated long coat, and the better cold tolerance of the double-coated short coat. Certainly all 4 variants are beautiful and have their own advantages.