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The extraction process of bioactive compounds from grape and apple pomaces was optimized using a response surface methodology to evaluate the effect of ethanol concentration, time and temperature on the extraction of total phenolic content, antioxidant activity by radical scavenging 2,2-diphenyl-1-picrylhydrazyl hydrate (DPPH) method and individual phenolics by high performance liquid chromatography (HPLC). Optimizing suggests that the best condition for total phenolic and gallic acid extraction from grape pomace was obtained in intermediate level (60% ethanol, 60 °C, 30 min) while 80% ethanol, 75 °C and 39 min was more efficient for p-coumaric acid extraction. For apple pomace the extract obtained with 50% ethanol at 75 °C and 39 minutes was more active by DPPH method and content of caffeic acid. Therefore, these abundant and inexpensive agro-industrial residues produced in Southern Brazil, are an important source of bioactive compounds that may be used as antioxidant substances in food and pharmaceutical industries.