Commonly used permanent identification methods for small rodents include ear tagging, ear notching, transponder implantation, and toe clipping. Each of these can be problematic in some circumstances.

Ear tagging and ear notching are not always reliably permanent. Ear tags, if not properly sterilized and placed, can cause irritation to the ear pinna and be pulled out. Ear notching uses a numbering code system that is limited to a maximum of three hundred and ninety-nine. Also, when animals fight, the ear can be ripped resulting in a loss of the tag or disruption of the pattern. Even excessive grooming can cause the pattern to be illegible or the tag to be removed. Also, these methods cannot be used on altricial neonates because their ears are still developing and are, therefore, too small.

Transponders are expensive and cannot be used on some very young animals because they are too big relative to the size of the animal. They can also be expensive when working with large numbers of animals that are kept for a short period of time.

Historically the solution to the identification of altricial neonates was to toe clip. This involves the removal of the first bone of certain toes. The Guide for the Care and Use of Laboratory Animals limits its use and states, “Toe-clipping, as a method of identification of small rodents, should be used only when no other individual identification method is feasible and should be performed only on altricial neonates”.

An alternative to all of the above identification methods is toe tattooing. Toe tattooing is a reliable and permanent identification method. Small rodents can be tattooed at any age. The toe tattooing procedure is easily taught to researchers, technicians, and animal care staff, with very good results. With the introduction of toe tattooing, toe clipping may be rendered obsolete.