The effect of different indigenous storage structures on the quality of cowpea (Vigna unguiculata) grains was carried out in the Savelugu / Nanton municipality of northern region from November 2012 to May 2013. 50% of total producers, 25 percent of retailers and 25 percent of consumers of cowpea grains in the Savelugu/Nanton municipality were randomly selected and interviewed from communities such as Tampion, Nanton, Savelugu, Pong Tamale, Diary, Zoggu, Nakpanzoo, Yepalsi, Gushei and Kanshegu. The structures used for storing cowpea grains were jute sacks, fertilizer sacks, clay pots, mud silos and cribs. The processing methods were threshing, drying, winnowing, transportation, application of chemicals and storage. The same quantity of grains were put in each of the storage structures and the parameters such as weight retained, temperature, relative humidity, number of insects and damage grains were determined every two weeks for quality analysis. The food nutrients such as carbohydrates, protein, fat, ash, moisture and fibre were analyzed at the Kwame Nkrumah University of Science and Technology Chemistry Laboratory, Kumasi. Finally, relevant conclusion and recommendations were made. Some of the relevant conclusions made were:Crib and clay pot were effective in maintaining the quality of grains in terms of weight retention, germination, insect protection, temperature, carbohydrates and proteins. Fertilizer sack, jute sack and mud silo were ineffective in maintaining the quality of cowpea grains. It was recommended that the crib and clay pot with little modification of fertilizer and jute would be good for cowpea over five month’s storage.