New synapse formation may underlie learning and memory. To examine specific synaptic plasticity by motor learning, we conducted quantitative analysis of synapses between parallel fibers and Purkinje cell dendritic spines in cerebella of rats trained to complete various obstacle courses. Synapses between parallel fibers and Purkinje cell spines were classified into single synapse boutons, multiple synapse boutons, and multiple synapse spines by their different contact features. Acrobat-trained animals had more single and multiple synaptic boutons, without change of multiple synapse spines, than motor control animals. These results may suggest that motor learning induces specific synaptogenesis and Purkinje cell spines are primary sites in motor learning-dependent cerebellar synaptic plasticity.