This study describes the levels of interleukin-1 alpha (IL-1 alpha), tumor necrosis factor alpha (TNF alpha) and interleukin-6 (IL-6) in the sera and parenchymal organs of various congenic mouse strains infected with Borrelia garinii. A significant elevation of inflammatory cytokine levels was found in the organs of C3H/HeN (H-2k) and B10.BR (H-2k) mice but not in those of BALB/c mice (H-2d). Focally produced cytokines can contribute to antimicrobial defense against these organisms. High levels of IL-1 alpha were observed in the sera of C3H/HeN, B10.BR and B10 (H-2b) mice infected with B. garinii and they were associated with the presence of spirochetes in the skin. Thus, susceptible mice demonstrated a stronger cytokine response than resistant mice. This study presents in vivo evidence that B. garinii infection affects the immunopathogenesis of Lyme disease.