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Starch physicochemical parameters and phase transitions were determined in flours of 10 advanced lines and cultivars of triticale (Cananea, Currency, Eronga, LA 24 Bve, LA 20 FCA, LA 83 FCA, Tatú, Tehuelche, Quiñé, and Yagan). Starch behavior was also analyzed during the baking of cookies prepared with triticale flours. Starch granule size, crystal type patterns, and size distribution were determined by light microscopy, X‐ray diffraction, and gel‐permeation chromatography, respectively. Two types and sizes of starch granules with characteristic A‐form crystals were obtained in all samples tested. The Quiñé cultivar showed the lowest extent of starch crystallinity. Only a monophasic endotherm was found by differential scanning calorimetry for water content >50–60%. Gelatinization temperature and enthalpy values varied significantly among samples. A biphasic endotherm was detected for water contents between 35 and 60%, and no endothermic transitions were observed for water levels <35%. Only one endotherm corresponding to starch gelatinization was detected in baked cookies prepared with five triticale flours. In all samples, the highest enthalpy of gelatinization of starch was detected for the cookie surface, whereas the highest gelatinization temperature was observed for the center. These differences may be attributed to the presence and content of the solutes in cookie dough and also to the degree of starch gelatinization during the cooking process.