Chlamydophila abortus (C. abortus) is one of the most important causative agents of enzootic abortion which has been caused a serious economic problem in domesticated and wild ruminants world wide. This study was aimed to diagnose C. abortus infection in aborted goats in Ras Suder Research Station (South Sinai) - Desert Research Center from 2004-2006. Twenty aborted cases from 130 pregnant nannies were recorded and examined serologically using complement fixation test (CFT). Eighty percent (16/20) of the aborted cases were serologically positive and 20% (4/20) randomly collected from apparently healthy pregnant nannies were also had antibodies against C. abortus. Pathological lesions were detected. Ten aborted fetal samples from serologically positive aborted nannies were subjected to diagnosis using Polymerase Chain Reaction (PCR) showed positive results at 119 bp. According to this result, PCR proved to be feasible, reliable, specific and sensitive diagnostic tool in diagnosis of C. abortus infection.