Rats trained on motor-skill learning tasks for 30 days were previously found to have more synapses in the volume of tissue proportional to a Purkinje cell than rats that exercised or were inactive. In the motor learning tasks, hooded rats were required to traverse an obstacle course requiring balance and coordination. Rats in two exercise groups were required to walk rapidly or allowed to run in activity wheels. Controls were relatively inactive in standard housing and handled once daily. Synapses were classified to determine which synaptic types changed in number across levels of the molecular layer in the paramedian lobule. The motor learning group had significantly more parallel fiber synapses and climbing fiber synapses per unit Purkinje cell reference volume than all other groups. There were also more synapses and more parallel fiber synapses per reference volume in the outermost than in the innermost molecular layer. The plasticity reported here occurs in vivo under normal physiological conditions. Excitatory synapses account for at least 80% of the synapses in the molecular layer. The results support prior predictions that parallel fiber synapses are modifiable during conditions of learning.