The aim of our research was to connect the detailed study of fruit anatomy of black crowberry (Empetrum nigrum) with identification and detection of the main non-anthocyanin polyphenolic compounds. Our experimental results showed that the highest accumulation of anthocyanin bodies occurred in mature fruits in outer layers during fruit development. The shape of the anthocyanin bodies was most often globular, spherical, hemispherical and intermediate types were present only occasionally. Mature cells of the gynoecium and pericarp generally contain anthocyanin bodies incorporated inside vacuoles. The observed compounds accumulated in cells were rutin, quercetin and catechins, resveratrol; coumaric, p-coumaric, caffeic, ferulic acids, gallic, vanilic, syringic, cinnamic and caffeic acids. These compounds were selected because of their proposed positive effects on health. The analyses of the polyphenolic spectrum showed predominance of ferrulic acid together with gallic acid and catechins with quercetin.The aim of our research was to connect the detailed study of fruit anatomy of black crowberry (Empetrum nigrum) with identification and detection of the main non-anthocyanin polyphenolic compounds. Our experimental results showed that the highest accumulation of anthocyanin bodies occurred in mature fruits in outer layers during fruit development. The shape of the anthocyanin bodies was most often globular, spherical, hemispherical and intermediate types were present only occasionally. Mature cells of the gynoecium and pericarp generally contain anthocyanin bodies incorporated inside vacuoles. The observed compounds accumulated in cells were rutin, quercetin and catechins, resveratrol; coumaric, p-coumaric, caffeic, ferulic acids, gallic, vanilic, syringic, cinnamic and caffeic acids. These compounds were selected because of their proposed positive effects on health. The analyses of the polyphenolic spectrum showed predominance of ferrulic acid together with gallic acid and catechins with quercetin.