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Some types of peripheral nerve injury lead to limb deafferentation, which leads to remodeling of body representation areas in different parts of the brain, such as in the primary motor cortex and primary sensory cortex. This plasticity is a consequence of several cellular events, such as the emergence and elimination of synapses in these areas. Beside neurons, microglial cells are intimately involved in synapse plasticity, especially in synaptic pruning. In this study, we investigated the transient changes in synaptic density in the primary motor and sensory cortex after different types of peripheral nerve injury, as well as the behavior of microglial cells in each scenario. Male C57/B6 mice were divided into a control group (no injury), sciatic-crush group, and sciatic-transection group, and treated with PBS or minocycline daily for different time points. Both types of sciatic lesion led to a significant decrease of synaptophysin and PSD-95 positive puncta counts compared to control animals 4 days after lesion (DAL), which recovered at 7 DAL and was sustained until 14 DAL. The changes in synaptic puncta density were concomitant with changes in the density and morphology of microglial cells, which were significantly more ramified in the primary motor cortex of injured animals at 1 and 4 DAL. Although the decreased synaptic puncta density overlapped with an increased number of microglial cells, the number of lysosomes per microglial cell did not increase on day 4 after lesion. Surprisingly, daily administration of minocycline increased microglial cell number and PSD-95 positive puncta density by 14 DAL. Taken together, we found evidence for transient changes in synaptic density in the primary motor, related to peripheral injury with possible participation of microglia in this plasticity process., Competing Interests: Declaration of competing interest None of the authors has any conflict of interest., (Copyright © 2022 Elsevier Inc. All rights reserved.)