BackgroundCrossed beaks have been reported to occur in Appenzeller Barthuhn, a local Swiss chicken breed. The assumed causes for this beak deformity which are also seen in other bird species including domestic chickens, range from environmental influences to genetic factors. The aim of this project was to characterize the prevalence, the phenotype, and the underlying genetics of crossed beaks in Appenzeller Barthuhn chickens.ResultsThe estimated prevalence of 7% crossed beaks in Appenzeller Barthuhn was significantly higher compared to two other local Swiss chicken breeds. A breeding trial showed significantly higher prevalence of offspring with deformed beaks from mating of affected parents compared to mating of non-affected parents.Examination of 77 Appenzeller Barthuhn chickens with crossed beaks showed a variable phenotype presentation. The deviation of the beak from the median plane through the head ranged from 1° to 61°. In more than 60% of the cases, the upper and lower beak were bent in the same direction, whereas the remaining cases showed different forms of crossed beaks. Computed tomographic scans and bone maceration of the head of two chickens with crossed beaks revealed that the maxilla and the mandibula were affected, while other parts of the skull appeared to be normal.The gene LOC426217, a member of the keratin family, was postulated as a candidate gene for beak deformity in domestic chickens. Sequencing of the coding region revealed two significantly associated synonymous variants for crossed beaks in Appenzeller Barthuhn chickens. A genome-wide association study and a comparative analysis of runs of homozygosity based on high-density SNP array genotyping data of 53 cases and 102 controls showed no evidence of association.ConclusionsThe findings suggest a hereditary cause of crossed beaks in Appenzeller Barthuhn chickens. However, the observed variation in the phenotype, together with the inconclusive molecular genetic results indicates the need for additional research to unravel the genetic architecture of this beak deformity.Electronic supplementary materialThe online version of this article (10.1186/s12917-018-1398-z) contains supplementary material, which is available to authorized users.