Ovine enzootic abortion is an infectious and contagious disease clinically characterized by abortion and weak neonates, affecting sheep and goats. The etiological agent is Chlamydophila (C.) abortus, which is considered one of the most common animal pathogens of small ruminants; it has important economic implications and represents a significant zoonotic risk. Clinical diagnosis is often difficult because the clinical signs and the pathological lesions are not specific for C. abortus infection, in fact they can also be observed as a result of infections with other abortifacient agents. Moreover, the involvement of the laboratory is necessary to perform the definitive diagnosis. One hundred and seventeen vaginal swabs from sheep with clinical signs related to chlamydial infection were examined by a PCR-RFLP assay that demonstrated high specifity and sensitivity. Six samples were positive for C. abortus. Vaginal swabs are easy to handle and allow to deal with biohazardous material in safety conditions.