Minor compounds in vegetable oils are of health interest due to their powerful biological antioxidant properties. In order to extend the shelf life of sunflower oil, it is generally subjected to a refining process that can affect these desirable compounds. The main purpose of this study was to determine the effect of this chemical/physical refining process on selected minor components of sunflower oil in order to establish the nutritional quality and health properties of the oil. The oxidative stability, contents of fatty acids, tocopherols, phytosterols, reducing capacity, β-carotene, chlorophyll, and squalene were studied during six refining steps. Quantitative data showed the evolution of oil quality according to its degree of refinement. The results showed a significant decrease for all of the minor compounds analyzed, with losses in carotenoids of 98.6%, 8.5% in tocopherols, 19.5% in phytosterols and 45.0% in squalene. The highest reductions were recorded for the compounds that alter the most the visual aspects of the oil (waxes, carotenoids and chlorophylls) whereas reduction was limited for the compounds with no impact on the organoleptic quality. The losses in the compounds of health interest should be minimized by improving the refining processes and/or having a greater content of those molecules in crude oil by breeding new performing varieties.