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The development of rancidity is a major challenge in whole grain foods. Rancidity can develop in whole grain flour before processing as well as during storage of the finished products. The objective of this study was to determine the storage stability of whole wheat extrudates produced from flour stored in the freezer or at ambient conditions for 6 months. Two lots of whole wheat flour were divided into two portions. One portion was stored at ambient conditions (22 °C and 65% relative humidity); the other portion was stored in a freezer (-20 °C). After 6 months of storage the flours were extruded using a pilot scale Wenger twin screw extrusion system to produce a Ready-to-Eat puffed wheat crisp cereal. Cereals from each treatment were packaged in sealed foil laminate pouches and stored at ambient conditions up to 6 months. Flours and cereals were analyzed for free fatty acids and hexanal. After 6 months of storage, the whole wheat flour stored at ambient conditions contained significantly more free fatty acids (10.7 µmol/g) and hexanal (16.4 ppb) compared with the flour stored in the freezer (4.58 µmol/g and 1.9 ppb respectively); however, after extrusion the cereals were not significantly different for free fatty acids or hexanal (4.40 µmol/g vs 4.25 µmol/g and 3.47 ppb vs 3.47 ppb, respectively). After 6 months of storage the cereals were still not significantly different for these analytes (3.98 µmol/g vs 4.45 µmol/g; 9.77 ppb vs 10.1 ppb). Surprisingly, extrusion of “rancid” flour did not change the storage stability of extruded crisps compared with stored crisps from sound flour.