The warehouse receipt system for maize (Zea mays L.) was introduced in Uganda to enhance farmer access to markets and credit in order to increase the efficiency of the maize value chain and to improve smallholder incomes. Though, since the inception of the warehouse receipt system in Uganda, there has been low participation of smallholders selling their maize through this marketing channel. A study was done to examine the role of Farmer Organizations linking smallholders to maize markets in Eastern Uganda. The study was conducted in the eastern districts of Kapchorwa, Kween, Luuka, Iganga, Namutumba, Kaliro and Mayuge. The data was collected during the month of August 2013 for Kapchorwa and November 2013 for Agro-Ways. Primary data was collected from the farmers using the survey method. A standardized pre-tested questionnaire was used to collect data. Seventy warehouse receipt system users and non-users were purposively selected. The focus of the study was to establish the role of farmers’ organizations participating in the warehouse receipt system for maize through the examination of the critical factors influencing the performance of farmers’ organizations in linking smallholder maize farmers to the warehouse receipt system and the extent to which these factors affected the performance of Farmer’s Organization in accessing the warehouse. A Tobit model was used to determine the extent to which certain factors influenced the farmer organization performance in the warehouse receipt system. The proportion of maize taken to the warehouse was used a proxy for performance. Survey results showed that the size of the farmer organization (0.000), clear understanding of rules(0.000), ability to participate in decision-making(0.000), gender composition (0.000), distance to the warehouse (0.014) and access to finance (0.004) were the most significant factors that determined the performance of the group.