Potatoes ( L.) are a good dietary source of carbohydrates in the form of digestible starch (DS) and resistant starch (RS). As increased RS content consumption can be associated with decreased chronic disease risk, breeding efforts have focused on identifying potato varieties with higher RS content, which requires high-throughput analysis of starch profiles. For this purpose, freeze drying of potatoes has been used but this approach leads to inaccurate RS values. The present study objective was to assess the starch content (RS, DS and total starch (TS)) of three cooked potato genotypes that were dried using freeze drying and innovative drying techniques (microwave vacuum drying, instant controlled pressure drop drying and conductive hydro-drying) relative to freshly cooked potato samples. Depending on the genotype, all drying methods showed one or more starch measures that were significantly different from freshly cooked values. The combination of ultrasound and infrared assisted conductive hydro-drying was the only method identified to be associated with accurate assessment of DS and TS content relative to fresh samples. The drying treatments were all generally associated with highly variable RS content relative to fresh controls. We conclude that freshly cooked samples must be used for selecting varieties with a high proportion of RS starch as drying of cooked potatoes leads to unreliable RS measurements.