Methods of identification of animals

Choosing a reliable method of identifying individual animals is often an essential part of study design, and can also be important in maintaining breeding colonies of animals. Different techniques can provide either short-term or prolonged identification of individuals, and vary greatly in approach.

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Implantable electronic transponders provide a permanent and unique identification method for a wide range of species. The microchip is usually implanted subcutaneously in laboratory species, and its code can be read using a detector placed close to the animal’s skin. The technique is very reliable but is costly in comparison to some of the other available methods. There are also a number of different types of microchips, and some can only be read by the specific detector from the chip manufacturer. Microchips can also migrate from the site of original placement, and this can occasionally make the chip difficult to locate.


Tattoos are an effective and permanent means of identifying animals, providing they are applied competently. They are often placed inside the ear of larger animals, or on relatively hairless areas of skin such as the tail in rodents. The systems used vary greatly between establishments (Chen et al, 20161). The degree of restraint and the degree of discomfort can vary greatly and may require anaesthesia in order to be performed humanely and effectively. In the UK, if anaesthesia is required, then regulatory approval may be required.

Ear tags

Uniquely numbered metal tag
Fig. 1 Uniquely numbered metal tag

Ear tags are widely used in a range of species. In larger animals, they are generally reliable but may be removed either by a cage or pen mate or by contact with the cage or pen. In rodents, small, uniquely numbered metal tags (Fig. 1) can be used, but even when properly placed, removal by the animal or its cage mate is a frequent problem.

Ear clipping or punching

Mouse ear punch/notch code
Fig. 2 Mouse-ear punch/notch code

Ear clipping or punching is a widely used method of marking both large and small animals but is particularly popular as a means of identifying rats and mice. It is an easy and permanent means of identification, but fighting in rodents resulting in trauma to the ears can mask the identification code. The system used varies greatly from laboratory to laboratory (Fig. 2). If an ear notching scheme is applied within each cage, rather than across multiple cages, then a simpler code with fewer “notches” can be used. This has welfare advantages since the procedure causes transient pain. (Fig. 3) A specific advantage of this technique is that the tissue removed when marking GA rodents can be used for genotyping.

Marker pens

Fig. 3 Mouse-ear clipping

Non-toxic marker pens can be used to mark the fur, ears or tail of a range of species. Either multiple colours or multiple marks can be used to identify different individuals. Marks usually persist for a few days, but this varies greatly as animals may groom the area and remove the mark. However, this is an easy technique and particularly suitable for short-term (e.g. <24h) identification of animals. Where frequent monitoring occurs repeat marking can extend the life of a temporary mark.

Toe clipping

Toe clipping can be used as a means of identifying neonatal rodents, but its use is discouraged and micro tattooing of the digits provides a more humane alternative (Kasanen et al, 20112).

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Updated on 12th October 2020

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