Conventional methods of preparing tissue specimens for morphological investigation of the central nervous system suffer from inevitable artifacts caused by anoxia during the processing. In the present study we performed ultrastructural analyses of mouse cerebellar cortex using the in vivo cryotechnique (IVCr), which minimizes ischemic artifacts of target organs through direct cryofixation in vivo. In molecular and Purkinje cell layers of the mouse cerebellum prepared with IVCr, considerably large extracellular spaces (ECS) were detected among cellular profiles and synaptic clefts. The ECS obtained with IVCr without ischemia were larger than those obtained with IVCr after 8-minute ischemia or a conventional quick-freezing method with fresh resected tissues (FQF), but did not decrease with IVCr after 30-second ischemia. By contrast, the parallel fibers observed with IVCr without ischemia were slightly smaller than those after 30-second ischemia, and significantly smaller than those prepared with IVCr after 8-minute ischemia or FQF. ECS were frequently preserved around synaptic clefts, although the rest were totally or partially enclosed with closely apposed glial processes. The estimated sizes of the ECS around synaptic clefts did not differ between the opened and enclosed synapses, suggesting that the opened synapses might be temporarily surrounded by glial sheaths dynamically extending or retracting throughout the perisynaptic ECS. These findings indicate IVCr to be useful for some morphological analyses of ECS in the central nervous system. The appreciable ECS around synapses would allow morphological and functional changes of neuronal and glial cells dynamically involved in synaptic remodeling or signal transduction.