Chlamydophila abortus is one of the major causes of infectious abortion in pregnant sheep (Enzootic Abortion of Ewes or EAE) worldwide. Organisms shed in infected placentas and uterine discharges at lambing time are the main sources of environmental contamination, responsible for transmission to susceptible animals and possible human contacts. In the present study, a newly developed test, based on a recombinant fragment of the polymorphic outer membrane protein POMP90 (rOMP90-4 iELISA) and one based on the VS2 region of the major outer membrane protein MOMP (MOMP VS2 iELISA) were compared using sera from C. abortus infected ewes, at different stages throughout pregnancy. The POMP iELISA detected antibody much earlier in pregnancy than the MOMP iELISA, which like the complement fixation test detected antibody only at the time of abortion or lambing. No anti-MOMP antibody response could be detected in three of seven experimentally infected ewes. Furthermore, the POMP iELISA detected antibody in an animal that seroconverted during the course of the study, which the MOMP iELISA failed to detect. Overall, the results show that the POMP90-4 iELISA is considerably more sensitive than the MOMP VS2 iELISA for identifying animals infected with C. abortus. Earlier detection of infection will allow appropriate control measures to be taken to reduce environmental contamination, thus limiting the spread of infection, financial losses and the possible risks of zoonotic transmission to humans.