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The aims of this study were to find out if organic apple juice (AJ) contained higher contents of polyphenols or patulin compared to conventional AJ, and if higher storage temperature before processing increases patulin content in juice. AJ was pressed from Estonian, Danish and Norwegian apples. Additionally, three cultivars from Estonian organic and conventional orchards were stored at 3±2 °C and 9±2 °C before processing. Patulin, polyphenol content and antioxidant capacity were determined in pasteurized juices. In 2015, 33% of conventional (n=6) and 46% of organic (n=11) juices contained patulin; two of the organic juices above the legal limit (191 and 64µg l-1). In 2016, none of the AJs contained patulin. Patulin occurrence was more affected by weather conditions two weeks before harvest than by cultivation system and apple storage temperature. Polyphenol content was higher in organic than in conventional juices and was reduced at higher apple storage temperature.