Mice are exquisitely sensitive to infection with encapsulated B. anthracis strains, even in the absence of toxins. Bioluminescence imaging shows that the lungs are the terminals targets before death, whatever the route of infection: cutaneous, inhalational or digestive. In this study, we addressed the pathophysiological mechanisms of this phenomenon during a cutaneous infection in the absence of toxins. Ultrastructural analysis before the appearance of any clinical signs shows a high density of encapsulated bacteria colonizing the alveolar capillary network. Histological analysis when clinical signs were patent, just before death, showed lung tissue damage, with bacteria localized in alveolar capillaries and spaces along alveolar cells. Bronchiolar epithelium injury and intra-alveolar hemorrhages were also observed. Using functional approaches, we detected hypoxia of blood vessel endothelial cells in the lung, and multifocal hypoxic zones in the brain parenchyma, associated with neurological signs at the time of death. During the bacteriemic phase of infection, we determined that the bacteria circulating in blood presented as chains of circa 13μm in length with a mean of 4 bacteria per chain. To address the mechanisms of lung colonization, we mimicked this phase of infection by intravenous inoculation of bioluminescent bacteria of a similar chain length; the bacteria were immediately trapped within the lung capillary network. Encapsulated bacteria of shorter length were not sequestered and trapping was decreased in the absence of the capsule surrounding the bacilli. In conclusion, we show that the high pathogenicity of B. anthracis in the absence of toxins is most probably linked to physical sequestration of blood-circulating encapsulated bacilli of a given length. Clearly, in the case of anthrax, the toxins produced by the trapped encapsulated B. anthracis will add locally their deleterious effects. Controlling the lung-targeted pathology would be beneficial for the prognosis of anthrax infection.