Background and Objective Adventitious presence (AP) or unintentional commingling of genetically modified (GM) grain in non‐GM grain lots is a concern for stakeholders who wish to produce non‐GM grain and grain‐based products. AP that exceeds tolerance levels results in the loss of product marketability as “non‐GM” and subsequent loss of a premium market price. The objective of this study was to evaluate the US commodity corn supply chain using Fault Tree Analysis (FTA) and Failure Mode and Effect Analysis (FMEA) to assess factors contributing to AP in supply chains that handle both GM and non‐GM products. Findings Systematic analysis of the farm‐to‐feed supply chain identified key processes and actors involved. FTA identified 27 factors potentially contributing to AP along with their root causes. Ranking of factors using FMEA prioritized 14 factors as “critical” with a comparatively higher likelihood of occurrence and impact on AP levels. Conclusions AP contributing factors were found across the supply chain, indicating that successful segregation relies on all supply chain participants. Identification and prioritization of critical factors make it possible to target resources to a small number of significant factors to attain low AP levels rather than distributing resources across the entire set of factors. Significance and Novelty This study is an initial attempt to provide insights into the assessment and management of AP in the grain and feed supply chain with a novel application of FTA and FMEA techniques.