Carnitine palmitoyltransferase (CPT) was studied in muscle homogenates of two patients with muscle CPT deficiency heterozygous for the Ser-113 Leu mutation in the CPT II gene. Total CPT activity was normal in both patients but was almost completely inhibited by malonyl-CoA and Triton X-100 whereas in controls 38% and 58% of total activity remained in the presence of malonyl-CoA and Triton X-100, respectively. The addition of 1% Tween 20 abolished about half of the activity in patients but not in controls. Preincubation of muscle homogenate with trypsin slightly increased the total activity and rendered the activity greatly insensitive to inhibition by malonyl-CoA in both patients and controls. The data support the view that in patients with muscle CPT deficiency both CPT I and II are active, but that CPT II is abnormally accessible to inhibition by malonyl-CoA.