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The beneficial effects of nut consumption on human health have been largely confirmed. However, these benefits are variable as a wide range of factors have main influence on the nutritional composition of nuts. This is the case of the specific cultivar considered, as different almond, pistachio and walnut cultivars produce nuts with differentiated composition. Still, there are factors beyond cultivar effect that need to be further analysed. This is the case of weather conditions during nut development. In this study, we evaluate the influence of genotype and the crop year (weather conditions) on nuts health-promoting properties. With that purpose, the nutritional composition of 29 different nut cultivars has been evaluated during two consecutive crop years (2015-2016). The objective of this study was to evaluate in which extend uncontrollable weather conditions during nut development affect the nutritional composition of almonds, pistachios and walnuts. This variability was compared to that resulted from the use of different cultivars. Results show that by using different cultivars, some of the main nutritional parameters of nuts, such as oil content or concentration of linoleic can be controlled. However, for some of the decisive factors on nut nutritional quality, such as protein content, phytosterols concentration and presence of minerals such as iron or sulphur, the weather conditions of the considered crop year are determinant. In this scenario, the health-promoting properties of nuts might be compromised by the climate variability associated to climate change.