Apricot fruits are a favorite for consumption; however, their kernels are a rich source of nutritionally interesting substances, too. Nevertheless, in processing of apricots, the kernels remain often unused. In this study, 32 cultivars of different origin were analyzed for their protein content and content of secondary metabolites (phenolics and flavonoids). The weight and taste of kernels were assessed and these data were summarized for an evaluation of the attractiveness of the studied apricot kernels. Results showed that the protein content of kernels ranged from 14.56% to 28.77% and did not depend on the origin or weight of kernel, or taste. In addition, total phenolic (63.5–1277.3 mg GAE/100 g DW) and total flavonoid (0–153.1 mg CE/100 g DW) contents and antioxidant capacity (483.4–2348.4 mg TE/100 g DW) were measured in kernels. In conclusion, the Czech hybrids LE-5959, LE-5500 and French cultivar Koolgat are prospective for kernel processing and consumption because of their high protein content and sweet taste. Hybrid LI-3-6, originating in China, showed high protein content as well but because of bitter taste could be useful rather in medicine.