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Summary: Contaminant seeds in crop seed lots constitute a pathway for plant species introduction into new areas, and these non‐native weeds may be an environmental problem if they become invasive. Seed certification is a process that regulates and guarantees the quality of seed lots, including their purity. In this study, we assessed weed contamination in certified and non‐certified seed lots (n = 116) from 12 crop species commonly cultivated in the Balearic Islands. Contaminant seeds were separated using sieves, and then manually under a stereomicroscope, before they were germinated to confirm taxonomic identity. Weight, number and diversity of the contaminant seeds per kilogram of seed lot, number released per hectare according to sowing rate, and taxonomic identity and biogeographical origin of contaminant species were recorded. Although certification reduced the number of contaminant seeds in the seed lots, it did not entirely eliminate contaminants, because we found up to 2000 contaminant seeds kg−1 of certified ryegrass and sulla. Overall, contaminant seeds represented 118 taxa; of which, 82 were identified to species level, 70% of species were native, 19% were cultivated, and 11% were non‐native. Two of the identified taxa were first records for the Balearic Islands. In conclusion, contaminant seeds in imported crop seed lots represent a non‐negligible pathway for plant species introduction. [ABSTRACT FROM AUTHOR]