Background Although bariatric surgery (BS) is considered safe, concern remains regarding severe post-operative adverse events and mortality. Using a national BS registry, the aim of this study was to assess the incidence, etiologies, and risk factors for mortality following BS. Methods Prospective data from the National Registry of Bariatric Surgery in Israel (NRBS) including age, gender, BMI, comorbidities, and surgical procedure information were collected for all patients who underwent BS in Israel between June 2013 and June 2016. The primary study outcome was the 3.5-year post-BS mortality rate, obtained by cross-referencing with the Israel population registry. Results Of the 28,755 patients analyzed (67.3% females, mean age 42.0 ± 12.5 years, and preoperative BMI 42.14 ± 5.21 kg/m 2 ), 76% underwent sleeve gastrectomy (SG), 99.1% of the surgeries were performed laparoscopically, and 50.8% of the surgeries were performed in private medical centers. Overall, 95 deaths occurred during the study period (146.9/100,000 person years). The 30-day rate of post-operative mortality was 0.04% ( n  = 12). Male gender (HR = 1.94, 95%CI 1.16–3.25), age (HR = 1.06, 95%CI 1.04–1.09), BMI (HR = 1.08, 95%CI 1.05–1.11), and depression (HR = 2.38, 95%CI 1.25–4.52) were independently associated with an increased risk of all-cause 3.5-year mortality, while married status (HR = 0.43, 95%CI 0.26–0.71) was associated with a decreased risk. Conclusion Mortality after BS is low. Nevertheless, a variety of risk factors including male gender, advanced age, unmarried status, higher BMI, and preoperative depressive disorder were associated with higher mortality rates. Special attention should be given to these “at-risk” BS patients.