SAS (sleep apnea syndrome) is a prevalent chronic disorder characterized by intermittent hypoxia and sleep fragmentation, and has been widely observed in association with gastrointestinal conditions such as GERD (gastroesophageal reflux disease) and colorectal cancer. However, previous studies encountered methodological constraints, leaving the shared genetic underpinnings unclear. To investigate the shared genetic architecture and causal relationship between gastrointestinal diseases and SAS, comprehensive genetic analyses were conducted. Large-scale GWAS summary statistics were integrated with advanced statistical genetics methods for the combination of data on both gastrointestinal diseases and SAS. A genome-wide cross-trait analysis assessed genetic correlations, identified shared loci, examined expression-trait associations, and inferred causal associations. Significant genetic correlation were found between GERD and SAS, gastroduodenal ulcer and SAS, chronic gastritis and SAS, and IBS (irritable bowel syndrome) and SAS. A cross-trait meta-analysis was conducted to pinpoint shared loci. Summary-based SMR (Mendelian randomization) was employed to predict causal genes associated with both gastrointestinal diseases and SAS. MR (Mendelian randomization) supported the causal roles of GERD in SAS. An intrinsic connection between gastrointestinal diseases and SAS has been demonstrated. The genetic relationship and causal effect of gastrointestinal diseases in SAS underscore the critical role of gastrointestinal health in managing SAS. Further investigation is warranted to elucidate the underlying mechanisms and implications for treatment.