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[Background] Flavan‐3‐ol compounds are important secondary metabolites which show high antioxidant activity and are responsible for bitterness and astringency of food products. The aim of this work was to evaluate the potential for selecting grape materials with higher seed flavanol content from a breeding population. The composition and content of flavan‐3‐ols from 151 genotypes obtained from crossing wine grape varieties was evaluated by UPLC in three consecutive years. [Results] Chromatograms of flavan‐3‐ol compounds showed the same 12 compounds for all samples, but quantitative differences were observed between genotypes as well as parental varieties. The most abundant compounds were (−)‐epicatechin and (+)‐catechin followed by proanthocyanidins A2 and B2. Progeny showed higher values than the parental genotypes for every detected compound indicating directional transgressive segregation. With these results genotypes with as much as five times more flavanols than their parents could be identified. The year effect was significant; however, high correlations between years for each compound indicated that there is a strong genetic component in the determination of flavanol content. [Conclusion] Higher contents of seed flavan‐3‐ols can be obtained by hybridisation, and those genotypes could be used for extracting healthy phytochemicals, adding value to seeds as a sub‐product in wine elaboration, This work was funded by the Government of La Rioja through the FOMENTA 04/08 research project. We also thank the Instituto de Estudios Riojanos for its financial support. Shiren Song was awarded a MAE‐AECID fellowship for 3 years. We are grateful to Viveros Provedo for grapevine management and assistance in collecting berry samples. We thank the collaboration of Isidoro Laguna, Gustavo Escudero and Aleceia Bermejo for their technical assistance with seed extraction.