Recently, the waddles (wdl) mouse was identified as a carbonic anhydrase VIII (Car8) mutant. The mutation is associated with marked deficiency of Car8, an inositol triphosphate receptor 1-binding protein expressed at high levels in cerebellar Purkinje cells. To help unravel the molecular aberrations contributing to motor dysfunction in wdl mice, cerebellar gene expression profiles were examined in the mutants and their wild-type littermates. Genes involved in signaling, cell division, zinc ion-binding, synapse integrity and plasticity were downregulated in wdl mice. Several of the upregulated genes encode proteins that function in the Golgi apparatus which suggests that Car8 deficiency has important effects on synaptic vesicle formation and transport.