NPGMA's Non-GMO program has created a standard with requirements for traceability, segregation, and GMO testing. Companies must meet a 0.9% GMO threshold for finished products, which is the EU threshold for GMO labeling and is increasingly recognized as a standard GMO threshold by food and grain companies. There is also a 5% GMO threshold for animal feed.

NPGMA Non-GMO certification also utilizes elements of global and domestic GMO labeling regulations, including EU and Vermont GMO labeling requirements. It requires risk assessment-based unannounced audits and unannounced chain of custody sampling. NPGMA certification also gives credit for food safety quality system best practices including segregation, traceability, and supplier approval and monitoring programs.

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