In 2006, Uganda adopted the Reaching Every District strategy with the goal of attaining at least 80% coverage for routine immunizations in every district. The development and utilization of health facility/district immunization microplans is the key to the strategy. A number of reports have shown suboptimal development and use of microplans in Uganda. This study explores factors associated with suboptimal development and use of microplans in two districts in Uganda to pinpoint challenges encountered during the microplanning process.