We have identified a novel missense mutation in the carnitine palmitoyltransferase II (CPT II) gene in a child with CPT II deficiency characterized clinically by episodes of myalgia and myoglobinuria induced by intercurrent febrile illnesses. The patient was heterozygous for a G-to-A substitution at codon 487, changing an encoded glutamic acid to a lysine (E489K), while the other allele carried the common S113L mutation. This case enlarges the spectrum of mutations in patients with CPT II deficiency, and confirms the association of the S113L mutation with the muscular form.