Cystatin C (CC), a cysteine protease inhibitor involved in protein degradation, is a marker of Bunina bodies in lower motor neurons in amyotrophic lateral sclerosis (ALS). TAR-DNA binding protein-43 (TDP-43)-immunoreactive inclusions are also histological hallmarks of ALS but whether CC is found in motor neurons with or without TDP-43-positive inclusions in ALS is not known. To determine whether inclusion body formation affects cytoplasmic CC immunoreactivity, we examined spinal cords from 9 ALS patients and 12 control subjects by immunohistochemistry. Most anterior horn cells (AHCs) showed moderate to intense immunoreactivity in controls, whereas CC immunoreactivity was markedly decreased in AHCs in ALS cases. The proportion of CC-immunolabeled AHCs was reduced regardless of whether they contained Bunina bodies. In contrast, the proportion of CC-immunolabeled AHCs was significantly reduced in those with TDP-43 inclusions. Cystatin C immunoreactivity of astrocytes in the spinal gray matter and white matter in ALS was significantly decreased compared with controls. These findings suggest that the formation of TDP-43 inclusions, but not of Bunina bodies, may be linked to the content of CC in spinal motor neurons and that perturbations in endogenous levels of CC in neuronal and glial cells may be part of the neurodegenerative processes in ALS.