Introduction: Congenital anomalies (CA’s) of most of the gastrointestinal tract have been linked causally with prenatal or community cannabis exposure. Therefore, we studied this relationship in Europe. Methods: CA data were from Eurocat. Drug-use data were sourced from the European Monitoring Centre for Drugs and Drug Addiction. Income data were taken from the World Bank. Results: When countries with increasing rates of daily cannabis use were compared with those which were not, the overall rate of gastrointestinal CA’s (GCA’s) was higher in the former group (p = 0.0032). The five anomalies which were related to the metrics of cannabis exposure on bivariate analysis were bile duct atresia, Hirschsprungs, digestive disorders, annular pancreas and anorectal stenosis or atresia. The following sequence of GCA’s was significantly linked with cannabis metrics at inverse-probability-weighted-panel modelling, as indicated: esophageal stenosis or atresia, bile duct atresia, small intestinal stenosis or atresia, anorectal stenosis or atresia, Hirschsprungs disease: p = 1.83 × 10−5, 0.0046, 3.55 × 10−12, 7.35 × 10−6 and 2.00 × 10−12, respectively. When this GCA series was considered in geospatial modelling, the GCA’s were significantly cannabis-related from p = 0.0003, N.S., 0.0086, 6.652 × 10−5, 0.0002, 71.4% of 35 E-value estimates and 54.3% minimum E-values (mEVv’s) > 9 (high zone) and 100% and 97.1% > 1.25 (causality threshold). The order of cannabis sensitivity by median mEVv was Hirschsprungs > esophageal atresia > small intestinal atresia > anorectal atresia > bile duct atresia. Conclusions: Seven of eight GCA’s were related to cannabis exposure and fulfilled the quantitative criteria for epidemiologically causal relationships. Penetration of cannabinoids into the community should be carefully scrutinized and controlled to protect against exponential and multigenerational genotoxicity ensuing from multiple cannabinoids.