Aims Neuromuscular junction (NMJ) is clinically important because abnormal neuromuscular transmission can cause myasthenic syndrome. Single-gene defects causing myasthenic syndrome are called as congenital myasthenic syndrome (CMS). Up to date, 20 disease CMS genes have been identified. Methods Recently, we have encountered a consanguineous family with CMS in Hong Kong. The proband has a clinically affected sibling and two clinically unaffected siblings. To identify the region of homozygosity (ROH), homozygosity mapping using high density single nucleotide polymorphism (SNP) genotyping arrays was performed. Whole-genome scan was performed with Affymetrix Genome-Wide Human SNP array 6.0 (Santa Clara, CA, USA) and the data were analysed with Genotyping Console Software (Affymetrix, Santa Clara, CA, USA) according to manufacturers’ protocols. Results A ROH of 20 MB was mapped on chromosome 6q15–21. This ROH consists of 138 genes and is the only ROH region that is present in all the clinically affected siblings and absent in all the clinically unaffected siblings. Discussions Currently, no known CMS genes are located on chromosome 6. We hypothesise a novel CMS gene is located in the ROH on chromosome 6. We will identify this novel gene by using whole exome sequencing.