Lyme disease, caused by Borrelia burgdorferi, is the most commonly reported vector-borne disease in the United States. Many patients treated for early Lyme disease incur another infection in subsequent years, suggesting that previous exposure to B. burgdorferi may not elicit a protective immune response. However, identical strains are almost never detected from patients who have been infected multiple times, suggesting that B. burgdorferi exposure may elicit strain-specific immunity. Probabilistic and simulation models assuming biologically realistic data derived from patients in the northeastern United States suggest that patients treated for early Lyme disease develop protective immunity that is strain specific and lasts for at least 6 years.