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Apples represent a greater proportion of the worldwide fruit supply, due to their availability on the market and to the high number of existing cultivar varieties and apple-based products (fresh fruit, fruit juice, cider and crushed apples). Several studies on apple fruit metabolites are available, with most of them focusing on their healthy properties’ evaluation. In general, the metabolic profile of apple fruits strongly correlates with most of their peculiar characteristics, such as taste, flavor and color. At the same time, many bioactive molecules could be identified as markers of a specific apple variety. Therefore, a complete description of the analytical protocols commonly used for apple metabolites’ characterization and quantification could be useful for researchers involved in the identification of new phytochemical compounds from different apple varieties. This review describes the analytical methods published in the last ten years, in order to analyze the most important primary and secondary metabolites of Malus domestica fruits. In detail, this review gives an account of the spectrophotometric, chromatographic and mass spectrometric methods. A discussion on the quantitative and qualitative analytical shortcomings for the identification of sugars, fatty acids, polyphenols, organic acids, carotenoids and terpenes found in apple fruits is reported. [ABSTRACT FROM AUTHOR]