Mycotoxins are low-molecular-weight natural products with great structural diversity produced as secondary metabolites by fungi. One of the principal toxic fungal metabolites is patulin (PAT), produced by over 30 genera of mold including species as Penicillium expansum or Penicillium griseofulvum, and normally related to vegetable-based products and fruit, mainly apple. These mold grow easily in damaged fruit or in derived-product as juices if storage conditions are deficient. Some of the most serious effects of PAT ingestion are agitation, convulsions, edema, ulceration intestinal, inflammation and vomiting. Thus, European Regulation 1881/2006 established a maximum content of 10 ppb in infant fruit juices, 50 ppb for fruit juices in adults and 25 ppb in fruit-derived products. Nowadays, the official analytical method for food adopted by AOAC International is HPLC with UV detection, using clean-up with ethyl acetate and sodium carbonate. However, the diverse drawbacks of this method (poor stability of PAT under alkaline extraction, poor resolution between PAT and co-extracted hydroxymethylfurfural) have originated interest in alternative options, such as LC methods coupled to mass spectrometry. In the last years, purification with molecularly imprinted polymers (MIP) started to be used, and are becoming promising materials for extracting different analytes present in food. Mycotoxins are too toxic or too expensive to be used as template molecules in MIP preparation. Template “bleeding” may be an additional problem, especially when dealing with very low detection levels. In the present work, a rapid and selective method based on magnetic molecularly imprinted stir-bar (MMIB) extraction has been developed for the isolation of PAT. A structural analogue, 2-oxindole, was used as dummy template. The polymer was grafted to the silanized glass surface of the stir bar.