Live bird markets (LBMs) are essential for marketing of poultry, but can be a hub for the rapid spread of diseases including avian influenza (AI). We assessed the status of biosecurity in 108 LBMs in 37 districts of Uganda. In all LBMs, carcasses were disposed of in the open and birds were introduced in the marketswithout initial quarantine. A high proportion of markets lacked a dedicated site for unloading of birds (86.1%) and a programme for disinfection (99.1%), had dirty feed/water troughs (93.5%), were accessed by stray animals (97.2%), and had sick and healthy birds (96.3%) or different bird species (86.1%) sold together. Differences in practices occurred among geographical regions and market location. Birds were more likely to be slaughtered in the open in urban compared to rural LBMs (OR=14.6, 95% CI: 1.50 - 142), while selling of un-caged birds was less likely in central compared to western region (OR=0.2, 95% CI: 0.04 - 0.17). Different poultry species confined in the same cage were more likely to be sold in urban (OR=22, 95% CI: 1.14 - 435) compared to rural markets. We conclude that LBMs in Uganda are a potential risk for spread of AI to poultry and humans.