Background: Consistent with the concept of the gut-brain phenomenon, observational studies have reported a pattern of co-occurring relationship between Alzheimer’s disease (AD) and a range of gastrointestinal tract (GIT) traits. However, it is not clear whether the reported association reflects a causal or shared genetic aetiology of GIT disorders with AD. While AD has no known curative treatments, and its pathogenesis is not clearly understood, a comprehensive assessment of its shared genetics with diseases (comorbidities) can provide a deeper understanding of its underlying biological mechanisms and enhance potential therapy development. Methods: We analysed large-scale genome-wide association studies (GWAS) summary data (sample size = 34,652 – 456,327) to comprehensively assess shared genetic overlap and causality of GIT disorders with the risk of AD. Further, we performed meta-analyses, pairwise GWAS analysis; and investigated genes and biological pathways shared by AD and GIT disorders.Results: Our analyses reveal significant concordance of SNP risk effects across AD and GIT disorders (Ppermuted = 9.99 × 10−4). Also, we found a significant positive genetic correlation between AD and each of gastroesophageal reflux disease (GERD), peptic ulcer disease (PUD), medications for GERD or PUD (PGM), gastritis-duodenitis, irritable bowel syndrome, and diverticular disease, but not inflammatory bowel disease. Mendelian randomisation analyses found no evidence for a significant causal association between AD and GIT disorders. However, shared independent genome-wide significant (Pmeta-analysis < 5 × 10-8) loci (including 1p31.3 [near gene, PDE4B], 1q32.2 [CD46], 3p21.31 [SEMA3F], 16q22.1 [MTSS2], 17q21.33 [PHB], and 19q13.32 [APOE]) were identified for AD and PGM, six of which are putatively novel. These loci were replicated using GERD and PUD GWAS and reinforced in pairwise GWAS (colocalisation) as well as gene-based analyses. Lipid metabolism, autoimmune system, lipase inhibitors, PD-1 signalling, and statin mechanisms were significantly enriched in pathway-based analyses. Conclusions: These findings support shared genetic susceptibility of GIT disorders with AD risk and provide new insights into their observed association. The identified loci and genes—PDE4B, CD46 and APOE, especially—and biological pathways—statins and lipase inhibitors, in particular—may provide novel therapeutic avenues or targets for further investigation in AD, GIT disorders, or their comorbidity.