Phytanic acid accumulates in excessive amounts in Refsum disease, a rare neurological disorder, due to a defect in its alpha-oxidation enzyme system in peroxisomes. The activation of phytanic acid to phytanoyl-CoA by phytanoyl-CoA ligase is a prerequisite for its alpha-oxidation. The studies described in this manuscript report that phytanoyl-CoA ligase in peroxisomes is an enzyme distinct from the previously reported acyl-CoA ligases.