Background Despite guidelines recommending perioperative thromboprophylaxis for patients undergoing general surgery, we have observed significant variations in its practice. This may compromise patient safety. Here, we quantify the heterogeneity of perioperative thromboprophylaxis across all major general surgical operations, and place them in relation to their risk of bleeding and venous thromboembolism. Methods Retrospective review of all elective major general surgeries performed between 1 January 2018 and 30 June 2019 across seven Victorian hospitals was conducted. Results A total of 5912 patients who underwent 6628 procedures were reviewed. Significant heterogeneity was found in the use of chemoprophylaxis, timing of its initiation, type of anticoagulant administered and application of extended chemoprophylaxis. These variations were observed within the same procedure, and between different surgeries and subspecialties. Contrastingly, there was minimal heterogeneity with the use of mechanical thromboprophylaxis. Oesophago-gastric, liver and colorectal cancer resections had the highest thromboembolic risk. Breast, oesophago-gastric, liver, pancreas and colon cancer resections had the highest bleeding risk. Conclusion Perioperative chemoprophylaxis across general surgery is highly variable. This study has highlighted key areas of variance. Our findings also enable surgeons to compare their practices, and provide baseline data to inform future efforts towards optimizing thromboprophylaxis for general surgical patients.