The one area that still vexes breeders is the effects of the hairless mutation. This is something they can not breed away from. Hairlessness is the defining characteristic of the breed, but in preserving that trait breeders are forced to deal with its effects, which include irregular dentition and unpredictable amounts of hairlessness.

Originally the first hairless dogs in meso-america would have resulted from spontaneous mutations, and as hairlessness is the result of a dominant gene it would have been perpetuated naturally. It also likely provided some kind of advantage; perhaps a greater resistance to external parasites, or a higher tolerance for heat. (Note: Contrary to a popular belief, these breeds do not have sweat glands - they pant to dissipate excess body heat like any other dog). What is clear is that the local population valued their hairless dogs. Their remains are found in graves and tombs and they are depicted on statues and wall reliefs in meso-american ruins. This human intervention and valuing likely contributed to the preservation of the hairless gene as they were more likely to use the hairless specimens for breeding stock than their coated brethren.

Modern efforts to modify the effects of this hairless gene have not been successful. While recent attempts to improve the quality of furnishings (crest and socks) in many breeding programs around the world appears to have increased the amount of extra hair on the hairless, it is unclear what mechanisms are at work as the hairless gene does not appear to respond consistently to established breeding practices. Traditional breeding practices suggest that selective breeding will usually result in the desired/or undesired trait being emphasized/or de-emphasized in progeny and future generations. For example, if you were looking to create a miniature version of a breed – you would consistently select the smallest examples of each litter and only breed from them, getting smaller and smaller dogs in turn, and so on until you had reached the desired size which will always breed true. However, with the hairless gene it is a bit of a crapshoot. The degree of hairlessness of the progeny is not apparently impacted to any great degree by the relative hairlessness of the parents. The progeny may exhibit all hair density levels in the same litter, or just one. Hairlessness can range from extreme (sparse crest and socks with an entirely hairless body), to moderate (dense crest and socks with just a strip of hair down its back), to extremely hairy (dense crest and sock with an almost fully coated body), and of course, the fully coated powder puff. It doesn't matter even if you breed extremely hairless to extremely hairless – you can get all extremely hairy puppies in the litter. The results are not consistent, nor repeatable, which suggests the variability of the expression of the hairless mutation may not be subject to the same "laws" of selective breeding that other traits seem to be.

The hairier dogs do seem to win in the ring, as their furnishings are more spectacular, and certainly as the body types have been stabilized so it appears that the degree of hairiness has gone up in the show ring. Perhaps in this case the apparent increase in hairiness is really a case of perception is reality. Breeders will by and large show and breed only those specimens that are winning/popular – and so while in the past the hairier dogs were not shown/promoted/bred to any great extent, today they are (with some notable exceptions who continue to concentrate on the more hairless specimens). This trend towards more furnishings may be at the root of the lack of apparent ubiquitousness of the very hairless specimens – who may still appear in the same numbers they always did in litters – they just may not be shown or bred to as extensively as in the past. Much more research is required to understand this hairlessness variability effect; How is it inherited? Are there are any modifiers? Are those modifers predictable and selectable?

Dentition

For hundreds of years, anecdotal evidence has strongly suggested a genetic link between the hairless trait and incomplete dentition. And now with the research cited above it is clear they are a genetic pair – you can't have one without the other. Just like with the degree of hairlessness challenge, attempting to breed away from irregular dentition in the hairless dog is not possible. A perfect hairless mouth has been the holy grail of many a breeding program, but it has never been produced with any degree of regularity.

Breeders and fanciers generally now accept that irregular dentition is part of the breed. While some may fret, the hairless dogs suffer absolutely no ill effects from this, and are able to eat what they want, chew what they want, play with what they want, like any other dog. In fact, many Crested owners will attest to their hairless Crested’s mousing abilities around the house, and their penchant to destroy many a chew toy.

Just like with body hair, because of various degrees of expressivity, the hairless mouth can vary from full dentition to several missing teeth. Any tooth may be present or absent. Regularly, baby teeth are not replaced with adult teeth; and where baby teeth have been missing, adult teeth can appear. The teeth that are present can be poorly rooted. In general, younger dogs will have more teeth but as they age the Crested may loose them sooner than other breeds

Additionally. the gene affects not just the presence and distribution of teeth in the mouth, but also their structure. The canines (both baby and adult) are almost always cone shaped to some degree, and will have a forward pointing aspect; these are frequently referred to as tusks. The shape of the incisors can vary considerably. Some are no more than little pegs protruding from the gums. Others are almost normal. Sometimes a full complement of narrow "pegs" can look as though they have been thrown in haphazardly. It must be noted that undershot, overshot and wry bites are not linked to the hairless trait. Jaw misalignment can be more difficult to assess if several teeth are missing, but it will affect the dog’s expression regardless of the presence or absence of teeth. When several teeth are missing, one can look at the jaw sideways to ascertain the jaws position.

Since the Powderpuff variety does not carry the hairless gene, full and normal dentition is expected.