This study, aimed to investigate Chlamydia abortus, C. pecorum, and C. psittaci in bovine, sheep, and goat abortions sent to the Konya Veterinary Control Institute diagnostic laboratory from various provinces in Central Anatolia and Mediterranean regions of Turkey between 2019 and 2022 via pathological and molecular methods. For this purpose, a total number of 150 abortions (from 58 cattle, 73 sheep, and 19 goats) were analysed via quantitative real-time polymerase chain reaction, histopathology and immunohistochemistry. The chlamydial DNA positivity rate was determined to be 24.00% via quantitative polymerase chain reaction analyses. According to the animal species, the positivity rate was 45.20% in sheep and 15.78% in goats. No cases positive for chlamydial DNA were found in the cattle abortions analyzed in the present study. When chlamydial agents were analysed on a species basis, C. abortus and C. pecorum were detected in 22.66and 1.33% of the cases, respectively. Among the animal species, 42.47% were C. abortus positive, whereas, 2.74% were C. pecorum positive in sheep. In the present study, the percentage of C. abortus-positive goats was 15.78%. and 22.66% of the Chlamydia spp. were positive according to immunohistochemical staining of aborted fetal lung, liver, heart, placenta and umbilical cord samples. This comparative study revealed that C. abortus was the most common chlamydial abortion agent in Türkiye. Chlamydial abortion agents cause abortion mostly in sheep in the region according to the animal species, and immunohistochemical staining contributes to the diagnosis of the agent at the Chlamydia spp. level.