Abortion in small ruminants is a large problem in many countries in the world including Jordan and cause severe economic losses to sheep and goats producers. Definite diagnosis and identification of the abortive agent and its associated pathological lesions have not been fully described. Therefore, twenty-five formalin-fixed and paraffin-embedded sheep and goat placentas taken at the time of abortion were examined for the presence of Chlamydia abortus and Brucella melitensis using gross, histopathological examination, immunohistochemistry and quantitative polymerase reaction (qPCR) for each of these agents. Immunohistochemistry successfully identified the etiologic agents of C. abortus and B. melitensis in 13 and 3 placentas, respectively, with adequate visualization of organisms in expected locations and corresponding lesions. Quantitative PCR for both agents was positive in 14 of the 25 placentas, with 5 being positive for both agents at the same time, and infrequent correlation of IHC with qPCR results. It is proposed that qPCR may be an overly sensitive technique for abortion diagnosis due to chronicity of infection and use of live vaccines and needs to be associated with the pathological lesions.