Late stages of borrelia Lyme disease infections may be difficult to diagnose because of unspecific symptoms and unreliable laboratory tests, being too unspecific or insensitive. The T cell immune response was thus evaluated in these patients by using a sensitive ELISPOT T cell assay that detects the secretion of IFN-gamma, i.e. a T helper 1 (Th1) response on the single-cell level. Three subcellular fractions of the Lyme borreliosis strain Borrelia afzelii were used for antigenic stimulation. The outer surface protein (Osp) fraction elicited the strongest response, discriminating between borrelia infections (n = 15) compared with other neurological diseases (n = 10) and normal controls (n = 12) (P = 0.0001). The more heterogeneous sonicated borrelia fraction also elicited a strong response, however, also in some of the controls. The flagellin fraction did not have a similar T cell-stimulating effect. When looking at subgroups of borrelia infections, central nervous system (CNS) infections (n = 7) revealed a lower T cell response in blood (P = 0.0128) compared with other borrelia manifestations (n = 8). Cerebrospinal fluid (CSF) lymphocytes were available from three patients with CNS borreliosis, and all showed a compartmentalization with higher responses to the Osp fraction in CSF compared with blood, also in the two patients without any intrathecal-specific antibody synthesis. The ELISPOT method is feasible for detecting a specific IFN-gamma T cell response in borrelia infections. This Th1 response may well be of pathogenic relevance.