Potato glycoalkaloids can reach levels that are harmful to human health. A rapid and reliable microwave assisted extraction method for quantitative analysis of α-solanine and α-chaconine content in raw potato and potato based products is presented. A chemical microwave was used to determine optimal temperature and pressure conditions for the extraction of α-solanine and α-chaconine from Idaho grown tubers and six commercially available mashed potato products. Recovery efficiency of glycoalkaloids was 37% greater by microwave assisted extraction (19.92 mg/kg glycoalkaloid) as compared to conventional solid/liquid methods (12.51 mg/kg glycoalkaloid). Optimal extraction of glycoalkaloids from potato samples dissolved in methanol was achieved using a microwave reactor set to 90 °C for ten minutes. The interior of Idaho grown tubers was determined to contain lower levels of glycoalkaloids (19.92 mg/kg dry weight; 6.5 ± 1.78 mg α-solanine and 13.40 ± 1.65 mg α-chaconine), as compared to commercial potato products (33.86–81.59 mg/kg).