Background The Iowa Rectal Surgery Risk Calculator estimates risk for proctectomy procedures. The Iowa Calculator performed well on NSQIP 2010–2011 training and 2005–2009 validation datasets, but was not prospectively validated and did not include low anterior resections. This study sought to demonstrate validity on new independent data, to update the calculator to include low anterior resection, and to compare performance to other risk assessment tools. Methods Non-emergent ACS-NSQIP proctectomy and low anterior resection data from 2010 to 2015 ( n  = 65,683) were included. The Iowa Calculator generated risk estimates for 30-day morbidity using 2012–2015 data. An Updated Calculator used 2010–2011 training data to include low anterior resection, with validation on 2012–2015 data. NSQIP data provided NSQIP Morbidity Model predictions and a custom web-script collected ACS-NSQIP Online Surgical Risk Calculator predictions for all patients. Results Proctectomy morbidity (not including low anterior resection) decreased from 40.4% in 2010–2011 to 37.0% in 2012–2015. Low anterior resection had lower morbidity (22.4% in 2012–15). The Iowa Calculator demonstrated good discrimination and calibration using 2012–2015 data (C-statistic 0.676, deviance + 9.2%). After including low anterior resection, the Updated Iowa Calculator performed well during training (c-statistic 0.696, deviance 0%) and validation (C-statistic 0.706, deviance + 7.9%). The Updated Iowa Calculator had significantly better discrimination and calibration than morbidity predictions from the ACS Online Calculator (C-statistic 0.693, P  < 0.001, deviance − 28.1%) and NSQIP General/Vascular Surgery Model (C-statistic 0.703, P  < 0.05, deviance − 40.8%). Conclusion When applied to new independent data, the Iowa Calculator supplies accurate risk estimates. The Updated Iowa Calculator includes low anterior resection, and both are prospectively validated. Risk estimation by the Iowa Calculators was superior to ACS-provided risk tools.