|Branched Chain α-Ketoacid Dehydrogenase (BCKD) enzyme complex have a role in metabolism of Branched Chain Amino Acid (BCAA). BCKDHA gene encoding the first subunit of these enzyme complex within mithochondrion. Mutation in BCKDHA gene caused deficiency of BCKD complex that caused Maple Syrup Urine Disease (MSUD). The aim of this research is to detect variability of BCKDHA gene in madura cattle using Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) method. According to migration pattern of single strand in PAGE 9%, there was four types found in exon 2 and 3 BCKDHA gene in madura cattle, that is A, B, C and D. There was two types of gene found in cattle that its origin from Bangkalan, which is A and C, whereas type that found in Sampang was four, which is A, B, C and D. The highest frequency in two locations is type A, in Bangkalan (83%) and in Sampang (50%).