Despite the importance of cowpea in Uganda as a leading legume, its production and improvement have not received much attention over the last two decades. Data was obtained on prices of grains of cowpeas on a weekly basis from FIT Uganda between 2008 to 2011 in Soroti, Lira and Kampala. Data collected was analyzed using descriptive statistics, particularly, frequencies and the measures of central tendency. Several approaches were used to investigate the degree of cowpea market integration in Uganda: bivariate correlation coefficients, co-integration and Granger-Causality tests were used to account for the complex interactions of prices in different markets. Results from these tests show that cowpea markets as a whole are not integrated. This is not a surprising result since it can be linked to the general lack of market information. Prices in different markets are not equally responsive to changes in the supply of cowpeas. The results obtained will assist in subsequent cowpea variety improvement actions and decisions.