Ear Punching

Punching or notching holes at various positions in the ears requires the use of an ear punch. The notches or holes correspond to a predetermined numbering code for individual animals. Ear marking is easy to read and produces little trauma to the animal, if done properly. Mice can be ear-punched as soon as the ear is “thinned out,” commonly around 15 days old. The tissue obtained from the ear punch may be used for DNA analysis for PCR analysis.

Rodents can be identified with the numbers 1 through 99 by putting a hole, a notch, a double notch, or any combination of these three marks in one or both ears.


Above is an example of a common numbering system:

  1. The marks on the animal’s right ear denote units or ones: 1, 2, 3, 4, 5, 6, 7, 8, 9, 0.
  2. The marks on the left ear denote tens: 10, 20, 30, 40, 50, 60, 70, 80, 90.
  3. The sample animal (bottom right) is number 53. The other animals shown illustrate the numbering system, as explained above.


  1. Soak the ear punch in alcohol to disinfect it before use and between animals.
  2. Place the device on the pinna of the ear (external ear) in a location where you want to mark the animal for identification.
  3. Press firmly to punch a circular hole through the ear.
  4. As you remove the punch, be careful not to rip the delicate membrane of the pinna. Gently separate the ear from the device.

Potential Problems

  • It is not uncommon for the holes or notches to grow closed over a period of time. It is important, therefore, to check the markings regularly to be certain the animal can still be identified accurately.
  • If group-housed mice fight, they may rip each others’ ears and cause ID information to be lost.

Please review our IACUC policy on Tissue Collection for Genotyping.

Information from the AALAS Learning Library