Fruits and by-products of fruit processing industry are produced annually in large quantities worldwide. Cherries and apple pomace are among the richest plant sources in bioactive compounds that are recognized for their beneficial effects on the human body. Appropriated methods of extraction (maceration, pressurized solvent extraction, ultrasoundassisted extraction, microwave assisted extraction), analysis (HPTLC, HPLC-UV-ELSD, HPLC-MS, SFC) and fractionation (CPC, HPLC semipreparative, liquid-liquid extraction) have been developed in order to extract, to identify and to purify bioactive compounds of cherry (Prunus avium) and pomaces of different apple varieties (Royal Gala, Golden Delicious, Granny Smith, Pink Lady). The results obtained during the research work indicate that these plant sources contain phenolic compounds (cherry, apple pomace) and triterpenic compounds (apple pomace) that can be used as ingredients for various food, pharmaceutical, cosmetic formulations etc.