Microglia are the first and main form of active immune defense in the nervous system. The immune status of microglia is directly correlated to their morphology. Therefore, microglia morphology is used to distinguish between active and surveilling microglia. For the actual paper, we used confocal laser scanning microscopy (cLSM) and two-photon laser scanning microscopy (2P-LSM), to investigate microglia morphology of 14-16 weeks old male, transgenic mice (n=6). After obtaining, in vivo and fixed tissue, single cells images, we manually tracked individually branch segments of normal microglia. The total number of branches and their overall length were analyzed. Additionally, the number and mean length of each branch order were measured. The overall microglia branching morphology was not different between the two acquisition methods. However, a higher number of fifth branches was observed using cLSM and 2P-LSM, in both fixed and in vivo tissue. Although results from the two methods are mainly comparable, small differences between them should be taken in consideration when formulating an activating∕surveilling conclusion that is purely based on pure microscopic findings. Furthermore, in our opinion, due to their highly dynamic nature, microglia should be carefully labeled as resting or active, taking also into consideration the imaging method used to obtain the data.