Hereditary canine spinal muscular atrophy (HCSMA) is a dominantly inherited motor neuron disease that produces muscle weakness and atrophy. Immunocytochemical and computer-imaging morphometric methods were used to compare early changes that occurred in dogs with HCSMA (n = 4) versus controls (n = 2). The size and number of neurons in the ventral horn and the number of motor neurons expressing choline acetyltransferase were quantitated. The density of all ventral horn neurons per micrometer squared in dogs with HCSMA was greater than controls, and there were more small neurons than in controls. Immunocytochemical methods revealed more small cholinergic neurons and fewer large cholinergic neurons in HCSMA than in controls, suggesting growth arrest in HCSMA or a shift in size class from large cholinergic neurons to small ones. The density of cholinergic neurons per micrometer squared was not significantly different between the two groups. Analysis of predicted distributions of cholinergic and noncholinergic neurons revealed that HCSMA cholinergic neurons were smaller and that, in some size classes, fewer neurons expressed choline acetyltransferase. These observations indicate that in HCSMA the motor neuron fails to achieve normal size and/or undergoes atrophy.