Effective identification of neonatal animals, especially small rodents is a challenge due to their small body size making it difficult to use common conventional identification methods such as ear tags or ear notches. Using microchip or numbering by permanent markers have limitations due to the cost or stability of the identification. Other methods such as a paw tattoo system used by some toxicologists for reproductive studies have limitation of the maximum usable number. Traditionally, digit amputation or toe clipping has been used for this purpose, however animal welfare aspects of this method is a significant concern. Here we describe a permanent identification by dot-tattoo marking of the digits using small gauge needles. The method was associated with minimal bleeding and no significant effect on neonatal growth rate and health. This method identification numbers of 1 to 9999 to be used. Therefore, we suggest that the method could be considered as an animal identification method for colony management of studies involving large neonatal production as well as reproductive or general toxicology studies.