Different biological and environmental factors, harvesting methods, transportation, storage time and the methods of storage affect agricultural product properties. As a result of climacteric nature and continuous physiological life of apple fruit, the biochemical changes can be important economical consequence. This study was designed to assess these changes and to understand how they can affect apple quality. In the first week of Oct. 2012 the fruits of two apple cultivars were harvested and stored in cold house (Malekan city, East Azarbaijan). Independent factors, storage time (0, 45, 90, 135 days) and cultivar (Golden delicious and Red delicious), were tested with factorial analysis in completely randomized design for some apple fruit characteristics. Results showed significant differences between cultivars in most biochemical characteristics. With increasing storage time, protein, soluble sugars, reducing and non-reducing sugar contents and the juice pH were significantly increased; however, titratable acidity, total soluble solids and electrical conductivity were decreased. Cold storage did not significant change insoluble sugars content. It can be concluded that, time dependent biochemical changes may occur with cold storage of apple fruits that may induce changes in quality of fruits.