The inedible part (stones, husks, kernels, seeds) of the tree fruits that are currently processed in various regions of Greece constitutes a huge portion of the fruit processing solid waste that remains underexploited. In this review, the existing scientific background for the composition and content of fruit stone and seed in bioactive ingredients is highlighted for olives, stone fruits and citrus fruits that represent the economically most important tree crop products of the country. The content of bioactive compounds may vary considerably depending on the quality of the raw material and the treatment during processing. However, both the hydrophilic and the lipophilic fractions of the seeds contain significant amounts of the primary and the secondary plant metabolites. Among them, phytosterols and several types of polyphenols, but also squalene, tocopherols and some other terpenoids with a unique structure are of particular importance for the utilization and valorization of stones and seeds. Official and scholar records about the current management practices are also presented to highlight the dynamics of the Greek fruit sector. Prospects for the regionalization of fruit seed wastes, in line with EU-promoted Research and Innovation Strategies (RIS) for Smart Specialization are critically discussed.
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