Nociceptive afferents and dorsal horn neurons undergo significant functional changes in pathological pain conditions. The structural remodeling of synapses of C afferents, which may contribute to the long-term maintenance of these changes, is not well understood. To investigate this issue, we used quantitative immuno-electron microscopy with serial sections to examine the structural changes of calcitonin gene-related peptide (CGRP)-immunopositive (+) and isolectin-B4+ (IB4+) axon terminals (boutons) and their pre- and postsynaptic elements in the rat medullary dorsal horn (MDH, trigeminal caudal nucleus). The study was conducted at 4 d (CFA 4-day) and 21 d (CFA 21-day) following complete Freund's adjuvant (CFA) injection into the vibrissa pad of the male Sprague Dawley rats, when thermal hyperalgesia was severe and had recovered, respectively. The ultrastructural parameters correlated with synaptic strength (bouton volume, mitochondrial volume, docked vesicle number, postsynaptic density area, dendritic spine number and size) in CGRP+ and IB4+ boutons and their postsynaptic dendrites increased significantly in the CFA 4-day group compared with control. The fraction of IB4+ boutons receiving axoaxonic synapses and the number of GAD65/67+ boutons involved in pre- and postsynaptic inhibition decreased significantly in the CFA 4-day group compared with control; these changes were restored to control levels in the CFA 21-day group. These structural changes in the C afferents and their pre- and postsynaptic elements in the MDH following inflammation may provide the morphological basis for the development and long-term maintenance of craniofacial inflammatory pain.