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Background Pathological gambling is a behavioural addiction with negative economic, social, and psychological consequences. Identification of contributing genes and pathways may improve understanding of aetiology and facilitate therapy and prevention. Here, we report the first genome-wide association study of pathological gambling. Our aims were to identify pathways involved in pathological gambling, and examine whether there is a genetic overlap between pathological gambling and alcohol dependence. Methods Four hundred and forty-five individuals with a diagnosis of pathological gambling according to the Diagnostic and Statistical Manual of Mental Disorders were recruited in Germany, and 986 controls were drawn from a German general population sample. A genome-wide association study of pathological gambling comprising single marker, gene-based, and pathway analyses, was performed. Polygenic risk scores were generated using data from a German genome-wide association study of alcohol dependence. Results No genome-wide significant association with pathological gambling was found for single markers or genes. Pathways for Huntington's disease ( P -value = 6.63 × 10 −3 ); 5′-adenosine monophosphate-activated protein kinase signalling ( P -value = 9.57 × 10 −3 ); and apoptosis ( P -value = 1.75 × 10 −2 ) were significant. Polygenic risk score analysis of the alcohol dependence dataset yielded a one-sided nominal significant P -value in subjects with pathological gambling, irrespective of comorbid alcohol dependence status. Conclusions The present results accord with previous quantitative formal genetic studies which showed genetic overlap between non-substance- and substance-related addictions. Furthermore, pathway analysis suggests shared pathology between Huntington's disease and pathological gambling. This finding is consistent with previous imaging studies. [ABSTRACT FROM AUTHOR]