Background: Access to insecticide-treated bed nets has increased substantially in recent years, but ownership and use remain well below 100% in many malaria endemic areas. Understanding decision-making around net allocation in households with too few nets is essential to ensuring protection of the most vulnerable. This study explores household net allocation preferences and practices across four districts in Uganda. Methods: Data collection consisted of eight focus group discussions, twelve in-depth interviews, and a structured questionnaire to inventory 107 sleeping spaces in 28 households. Results: In focus group discussions and in-depth interviews, participants almost unanimously stated that pregnant women, infants, and young children should be prioritized when allocating nets. However, sleeping space surveys reveal that heads of household sometimes receive priority over children less than five years of age when households have too few nets to cover all members. Conclusions: When asked directly, most net owners highlight the importance of allocating nets to the most biologically vulnerable household members. This is consistent with malaria behaviour change and health education messages. In actual allocation, however, factors other than biological vulnerability may influence who does and does not receive a net.