Alpacas are generally very organized and neat. When they defecate they usually designate one place, even if they need to walk farther away. They use a communal dung pile. Their waste is collected and used as garden fertilizer or even natural fertilizer.

Another factor that goes into alpaca hygiene is their tooth care. When observing the teeth of an alpaca, it is a good way to tell if they have a healthy digestive system. Alpacas have their full set of adult teeth by the age of six. Male alpacas have 32 teeth and female alpacas have 30 teeth.

Males have two extra teeth, called fighting teeth, but females only rarely have these. Alpacas have six lower incisors which help them bite off plants to chew. They do not have any upper incisors, but their mouths are lined up perfectly so that they have the ability to eat grass, hay, and plants.

There are warning signs to when an alpaca may have dental hygiene problems. One way to tell is if they take a while to chew their grass or hay or when they are eating, they continue to spill all their food and not keep it in their mouths. Another sign can be the poor body condition and if their cheeks are pushed in.

Alpacas use a communal dung pile, where they do not graze. This behaviour tends to limit the spread of internal parasites. Generally, males have much tidier, and fewer dung piles than females, which tend to stand in a line and all go at once. One female approaches the dung pile and begins to urinate and/or defecate, and the rest of the herd often follows.

Because of their preference for using a dung pile, some alpacas have been successfully house-trained.

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