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Biosecurity of highly infectious livestock diseases in East Africa intend to reduce disease spread but can impose an additional burden on rural, livestock-owning households. The embeddedness of livestock in household livelihoods, including for economic, social, and human health outcomes, suggests that social inequalities and practices in governance of risk can shape response to livestock disease. In this paper, we used novel data from an outbreak of the highly infectious, non-zoonotic foot-and-mouth disease (FMD) in 2018 to evaluate the importance of livestock quarantines for a sample of 231 rural, livestock-owning households across Uganda and Tanzania. We apply a governmentality perspective to quarantine restrictions to help explain how FMD has transboundary importance, while the social embeddedness of livestock in household livelihoods helps define how households enact social and economic relations to establish biosecurity as important. Summary statistics and seemingly unrelated logistic regression models demonstrate the transboundary effects of quarantine restrictions while logit models highlight the relationship between social inequalities and quarantine restrictions by movement (human, grazing, overall livestock) and sales (livestock products, live animals). Specifically, livestock movements and sales of live animals are reported as important across both Tanzania and Uganda despite formal quarantine policies only in Uganda. While infection with FMD was associated with market access, evidence of social inequalities (gender, income diversity) were related to overall movements and grazing. Empirically, the results extend prior evidence from the study areas to suggest that considerations for managing livestock disease risk should look beyond market access but consider the dynamics of social relations broadly. Additional research is needed on connecting quarantine policies to specific changes in household management behaviors and exploring ways to minimize reproduction of inequalities in disease response.