Although the WHO and other commentators have recommended distribution of free or highly subsidized ITNs for rapid scaling-up of net use, particularly for vulnerable groups, little is known about the extent of uptake across socio-economic groups and the factors influencing their access and utilisation. This study examined inequalities in use of ITNs and LLIN for Under5 children and pregnant women in Uganda. Coverage of indoor residual spraying and ITP during pregnancy was also examined. The Malaria indicator survey, 2009 data were used to estimate inequalities in use of ITN and LLINs while a total of 16 Focus group discussions involving household heads and women were conducted in Kabale (low malaria transmission) and Kayunga (high malaria transmission) districts to explore the community perspectives on barriers to utilisation of ITNs, IRS and IPTp. Ownership (45.6%) and utilisation of LLIN (32.1%) remain far below the 80% RBM target, and significantly pro-rich. Only 31% received at least 2 doses of recommended ITPp during ANC visit and just 5.5% of households reported use of indoor residual spray (IRS) over the past 12 months. Monetary cost of nets, discomfort during hot weather, and perceived risk of toxicity of ITNs greatly accounted for non-utilisation of ITNs.