Kainic acid (KA) model of epilepsy is a reliable tool to study temporal lobe epilepsy (TLE), the most common type of partial epilepsy in adults. Substantial body of data suggest that the KA-induced status epilepticus (SE) leads to several molecular and structural changes in the hippocampus, including sclerosis, sprouting of mossy fiber, reorganization of inter-neuronal networks, alterations in neuropeptide signaling, gliosis, and synaptic transmission dysregulation. However, no details on the ultrastructural changes, especially in relationship to synapses are available. This information is important in providing a comprehensive understanding of subtle changes that occur in this debilitating disease. Thus, in this study, applying electron-microscopic morphometric analysis, we evaluated the ultrastructural effects of KA on the CA1 region of the hippocampus, an area intimately involved in SE. The total number of synaptic vesicles (SVs), the number of docking SVs, the length of synapse active zone (AZ) and the number and area of presynaptic and postsynaptic mitochondria in axo-dendritic (excitatory) synapses were measured at 24 h, and 8 and 21 days after KA administration. Results indicate a decrease in the total number and docking of SVs, an increase in the length of AZ and the number and area of presynaptic and postsynaptic mitochondria, which were more prominent at 8 days after KA injection. The findings suggest a time-dependent ultrastructural changes in CA1 region of the hippocampus in an animal model of focal epilepsy.