As with almost anything, it's not a foolproof system. Although it's very rare, microchips can fail and become unable to be detected by a scanner. Problems with the scanners are also not common, but can occur. Human error, such as improper scanning technique or incomplete scanning of an animal, can also lead to failure to detect a microchip.
Some of the animal-related factors that can make it difficult to detect a microchip include the following: animals that won't stay still or struggle too much while being scanned; the presence of long, matted hair at or near the microchip implantation site; excessive fat deposits in the region of implantation; and a metal collar (or a collar with a lot of metal on it). All of these can interfere with the scanning and detection of the microchip.
See our literature review for guidelines on scanning procedures to reduce the chances of missing a microchip.