The increased interest in sea buckthorn (Hippophae rhamnoides L.) made it possible to investigate the antioxidant content in it. To address this issue, the presence of following antioxidant compounds were analyzed: trans-resveratrol, catechin, myricetin, quercetin, p-coumaric acid, caffeic acid, L-ascorbic acid (AA), and gallic acid (linear range of 50150 mu mol/L) in six different varieties of sea buckthorn berries extracts (sea buckthorn varieties: "Trofimovskaja (TR)," "Podarok Sadu (PS)," and "Avgustinka (AV),") received from two local Estonian companies. Trans-Resveratrol, catechin, AA, myricetin, and quercetin were found in extracts of sea buckthorn. Moreover, AA, myricetin, and quercetin contents were quantified. The biggest average AA content was found in TR (740 mg/100 g of dried berries, respectively). Furthermore, the same varieties gave the biggest quercetin content 116 mg/100 g of dried berries, respectively. For analysis, CZE was used and the results were partly validated by HPLC. Statistically no big differences in levels of antioxidants were consistently found in different varieties of sea buckthorn extracts investigated in this work.