A study was conducted to analyse the carotenoids by high-performance liquid chromatography (HPLC) using reversed-phase cross linked end-capping and to study the pigment content and composition in sea buckthorn products as well as in freshly harvested fruits from peach thees grown under organic and integrated farming conditions. It was found that carotenoids in fruits of both crops occur mainly esterified with fatty acids in form of mono- and di-esters. The major carotenoids were esters of zeaxanthin, lutein, β-cryptoxanthin and β-carotene. The major carotenoids showed different response to processing of sea buckthorn being highly sensitive to thermal treatments such as blanching, cooking and drying. Significant differences were found between peach varieties in their carotenoid content, whereas the impact of organic farming on carotenoids formation was found to be variety-dependent. Two of the three varieties examined in this work, when cultivated under organic farming conditions contained lower carotenoid level as compared to that found in the fruits of the same varieties but produced in integrated farms.