We characterized antigen-specific CD4 ؉ T cells in six patients with treatment-resistant Lyme arthritis, using an HLA-DRB1*0401 major histocompatibility complex (MHC) class II tetramer covalently loaded with OspA164-175, an immunodominant epitope of Borrelia burgdorferi. Direct analysis of OspA-tetramer binding CD4 ؉ cells in patients expressing the HLA-DRB1*0401 allele revealed frequencies of between <0.005 and 0.1% in peripheral blood (n ؍ 6), and between <0.005 and 3.1% in synovial fluid (n ؍ 3). OspAtetramer ؉ CD4 ؉ cells were directly cloned at 1 cell per well and expanded by mitogen and IL-2 on allogeneic feeder cells. As measured by [ 3 H]thymidine incorporation, 95% of 168 T cell clones from synovial fluid binding the OspA-tetramer were antigenreactive. Clones generated from peripheral blood revealed a different pattern of responsiveness when compared with clones generated from synovial fluid, as measured by proliferation, IFN-␥, and IL-13 secretion. These clones, selected on the basis of their peptide binding, also responded to whole protein, but with a different cytokine profile. Our studies demonstrate that MHC class II tetramers can be used in humans to directly identify, isolate, and characterize antigen-reactive T cells from an inflammatory compartment.