Rodent-borne and other communicable diseases are of particular concern to vulnerable populations in complex humanitarian emergencies. We assessed the risk of Lassa fever to refugees and humanitarian aid workers in the Forest Region of Guinea by trapping rodents and testing them for the presence of Lassa virus infection. Our study provides a point prevalence of Lassa virus-infected rodents in various refugee camps in Guinea, suggesting that the risk of disease may be highest in camps further south toward the border with Liberia. The methodology used represents a potential model for rapid public health assessments in the setting of complex humanitarian emergencies.