Persistent impairment of pulmonary defense reflexes is a critical factor contributing to pulmonary complications in patients with spinal cord injuries. The pulmonary chemoreflex evoked by activation of bronchopulmonary C-fibers has been reported to be abolished in animals with acute cervical hemisection (C2Hx). The present study examined whether the pulmonary chemoreflex can recover during the chronic injury phase and investigated the role of bronchopulmonary C-fibers on the altered breathing pattern after C2Hx. In the first protocol, bronchopulmonary C-fibers were excited by intrajugular capsaicin administration in uninjured and complete C2Hx animals 8 wk postsurgery. Capsaicin evoked pulmonary chemoreflexes in both groups, but the reflex intensity was significantly weaker in C2Hx animals. To examine whether spared spinal white matter tissue contributes to pulmonary chemoreflex recovery, the reflex was evaluated in animals with different extents of lateral injury. Linear regression analyses revealed that tidal volume significantly correlated with the extent of spared tissue; however, capsaicin-induced apnea was not related to injury severity when the ipsilateral-to-contralateral white matter ratio was <50%. In the second protocol, the influence of background bronchopulmonary C-fiber activity on respiration was investigated by blocking C-fiber conduction via perivagal capsaicin treatment. The rapid shallow breathing of C2Hx animals persisted after perivagal capsaicin treatment despite attenuation of pulmonary chemoreflexes. These results indicate that the pulmonary chemoreflex can recover to some extent following spinal injury, but remains attenuated even when there is moderate spinal tissue sparing, and that altered breathing pattern of C2Hx animals cannot be attributed to endogenous activation of bronchopulmonary C-fibers.