The response of guinea pigs experimentally infected with Coxiella burnetii organisms, the etiologic agents of Q fever, was obtained by the measurement of fever, circulating infectious C. burnetii cells, and anti-C. burnetii antibodies. The detection of antibodies by the enzyme-linked immunosorbent assay (ELISA) and traditional methods against phase I whole cells, phase II whole cells, and phase I lipopolysaccharide (LPS-I) (a virulence marker for phase I cells) antigens in the serum samples of infected animals revealed marked differences between intrastrain phase variants. Animals infected with the phase I Nine Mile strain produced a concomitant increase in temperature, circulating infectious C. burnetii cells, and antibodies against phase II cells, phase I cells, and LPS-I. At 15 weeks, a challenge of phase I-infected animals with viable phase I cells resulted in anamnestic antibody responses to phase I cells and LPS-I but not to phase II cells. Infection of animals with the phase II Nine Mile strain produced antibodies against only phase II cells. The challenge of phase II-infected animals at 15 weeks with viable phase II cells resulted in anamnestic antibody responses to phase I and phase II cells but not to LPS-I. Suppression of anti-phase II responses by the phase I challenge was apparent with only the ELISA, because the immunofluorescence, microagglutination, and complement fixation assays were insensitive to these changes. The sensitivity and specificity of the ELISA with whole-cell and the LPS-I antigens in the detection of phase-specific antibody revealed that avirulent phase II cells induced an immune response to phase I antigenic epitopes. Although the avirulent phase II cells were rapidly cleared by the host immune responses, they were sufficiently infective to induce antibody responses to both phase variants. Thus, in the occurrence of Q fever, any conventional serological technique that uses only phase II antigens may not provide a true incidence of naturally acquired infection with both phase I and II C. burnetii organisms.