A genome-wide association study aimed to identify novel single nucleotide polymorphisms (SNPs) associated with an increased risk of Barrett oesophagus as well as validate previously reported associations. Genotype analysis was performed in 10,158 patients with Barrett oesophagus and 21,062 controls. Two new SNPs were identified in genes that encode transcription factors involved in thoracic, diaphragmatic and oesophageal development, or proteins involved in the inflammatory response.