Despite its importance as a legume in Uganda, cowpea has not received much attention over the last two decades. A survey was conducted in northern, mid-northern and eastern agro-ecological zones of Uganda with the purpose of collecting baseline information on cowpea production, preferred attributes and production constraints. Data was collected from 306 randomly selected farmer respondents in four districts of Northern and Eastern Uganda using a structured questionnaire. Secondary data was also obtained on wholesale prices of cowpeas on a weekly basis from FIT Uganda from 2008 to 2011 for Soroti, Lira and Kampala markets. Data collected included: socio-economic characteristics of farmers, production practices, current varieties grown, and farmers’ preferences for the varieties, yields, marketing aspects and production constraints of cowpea. Data was analyzed using descriptive statistics particularly frequencies and the measures of central tendency. Chi-square and t-tests were used to elicit significant relationships between variables. Results showed that farmers in the region grew three common cowpea varieties. The majority (74%) grew Ebelat variety (Erect variety), 17% grew Ichirikikwai (spreading type) and 7% grew Alegi variety. Alegi was exclusively grown in Lira and Pader districts of Northern Uganda while Ebelat and Ichirikukwa were grown in Kumi and Soroti districts. Farmers preferred Ebelat and Ichirikikwai because of its quality traiting: include high grain yield, high leaf yield, seed color, early maturity and leaf texture. Pests, diseases, poor varieties, low market prices and price fluctuations were identified as constraints to cowpea production. Several approaches were used to investigate the degree of cowpea market integration in Uganda, namely: bivariate correlation coefficients, co-integration, and Granger-Causality tests. Results from these tests showed that cowpea markets in northern region (Lira) exhibit integration to the dominant markets in the Kampala. While Soroti did not exhibit market integration with Kampala and, this can be attributed to the fact that traders in this district engage in trade with the neighboring countries like Kenya and South Sudan. In addition to transportation cost, lack of an efficient information flow system resulted into lack of market integration between Soroti and Kampala. There is no leading market whose price changes influences all other markets since any price changes of cowpea in the markets studied are organized around more than one market. In order to understand these markets better, there is a need to analyze the value chain of cowpea in Uganda. Also, in order to realize the economic potential of cowpea in Uganda, infrastructure and accessibility to markets have to be improved.