To understand the therapeutic effects of crossing nerve transfer for brachial plexus injuries in human patients, we investigated cortical changes after crossing nerve transfer of brachial plexus using flavoprotein fluorescence imaging in mice. The distal cut ends of the left median and ulnar nerves were connected to the central cut ends of the right median and ulnar nerves with a sciatic nerve graft at 8 weeks old. Eight weeks after this operation, responses in the primary somatosensory cortex (S1) elicited by vibratory stimulation applied to the left forepaw were visualized. In control mice, direct responses (DRs) mediated via thalamic input was observed in the contralateral S1. Weak indirect responses (IRs) were also observed in the ipsilateral S1. In mice with crossing nerve transfer, DRs were observed in the ipsilateral S1. At the same time, clear IRs, which were not observed in control mice, were found in the contralateral S1. In our previous study, it was expected that DRs were initiated by thalamic inputs to layer 4, while IRs were secondarily initiated by callosal inputs from the ipsilateral S1 to the layer 2/3 in the contralateral S1. However, time courses of the normalized IRs in the contralateral S1 were comparable to those of DRs in the ipsilateral S1, although latencies required to reach half maximal amplitudes of IRs in the contralateral S1 were significantly shorter than those in the ipsilateral S1. In control mice, layer specific flavoprotein fluorescence responses were investigated using a macroconfocal microscope. The DRs in layer 4 were slightly larger in amplitude and faster in latency compared with those in layer 2/3. For understanding the origin of IRs after crossing nerve transfer, we are going to perform similar analyses regarding IRs in mice with crossing nerve transfer.