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Large-scale plant cultivation usually involves the use of pesticides. Apart from eliminating the target organism, the external chemicals may affect the metabolism of the crop plant. This may have implications for plants cultivated for specific medicinal compounds. In this study the effects of diverse fungicides on the metabolism of Narcissus pseudonarcissus cv. Carlton bulbs were investigated. N. pseudonarcissus cv. Carlton is being cultivated for the extraction of the alkaloid galanthamine. Fungicides typically used in Narcissus cultivation were applied in a field experiment. The aim was to determine whether fungicide applications changed the concentration of galanthamine in the bulbs. (1)H NMR spectroscopy allowed quantitative analysis of galanthamine and other metabolites in bulb extracts. Multivariate data analysis revealed changes in bulb metabolite patterns caused by fungicides. Bulbs treated before planting generally had higher levels of alkaloids, while foliar field applications caused lower alkaloid levels but altered carbohydrate metabolism. Within these groups, certain fungicide treatments caused changes in specific metabolites. This study shows that the fungicides used in Narcissus cultivation can cause a change in the metabolome still detectable in the bulbs after harvest. The standard cultivation practices in terms of fungicide treatment were found suitable for the production of N. pseudonarcissus cv. Carlton as raw material for galanthamine extraction. In the cultivation of medicinal plants for secondary metabolites the potential effect of pesticides and other agrochemicals should be taken into account., (Copyright © 2012 Elsevier Masson SAS. All rights reserved.)