Three-dimensional (3-D) information on nervous tissue is essential for the understanding of brain function. Especially, 3-D synaptic analyses on serial ultrathin sections with transmission electron microscopy (TEM) have contributed to the knowledge on neural plasticity associated with various pathophysiological conditions. The 3-D reconstruction procedures, however, not only require a great amount of expertise but also include time-consuming processes. Here, we carried out computer-assisted 3-D reconstruction of parallel fibre-Purkinje cell synapses based on 250 nm serial sections using high-voltage electron microscopy (HVEM). The 3-D synapse models were constructed more efficiently and rapidly compared with conventional serial TEM reconstruction. This result suggests that 3-D reconstruction with thicker sections and HVEM is a useful method to study synaptic connectivity.