Borrelia burgdorferi, the tick-transmitted etiologic agent of Lyme borreliosis, can colonize and persist in multiple tissue sites despite vigorous host immune responses. The extracellular matrix appears to provide a protective niche for the spirochete. Recent studies in mice suggest that B. burgdorferi interacts in various ways with collagen and its associated molecules, exploiting molecular and structural features to establish microcolonial refugia. Better knowledge of the genetic and structural bases for these interactions of B. burgdorferi with the extracellular matrix will be required before an understanding of the persistence of B. burgdorferi in the tissues and development of chronic infections can be achieved.