Approximately 1/3 of dogs with idiopathic epilepsy, a common neurological disease, are resistant to anti-seizure drugs (ASDs). Idiopathic epilepsy is diagnosed by excluding other diseases. Finding an IE biomarker may be beneficial for understanding, diagnosing, and treating the disease. Fractional anisotropy (FA) was measured in the corpus callosum and internal capsule of healthy dogs, dogs with IE responsive to ASDs, and dogs with IE resistant to ASDs. There were no significant findings between groups. Post-hoc analysis revealed a significant difference in corpus callosum FA between dogs with consistent versus variable seizures, F(1, 11) = 5.70, p = 0.036. Males had significantly higher corpus callosum FA than females, t(12) = -2.82, p = 0.015. Duration significantly and negatively correlated with the corpus callosum FA (r(12) = -0.58, p = 0.036) and internal capsule FA, r(12) = -0.74, p < 0.01. A larger sample size is needed to confirm findings.