In the present study, ocular chlamydial infections in pigs that originate from two different farming systems were investigated. In particular, the aim was to test pigs with and without clinical ocular symptoms for the presence of Chlamydiaceae and for linked infections with Acanthamoebae spp. possibly acting as vectors for Chlamydia or Chlamydia-like organisms. In a total of 181 pigs, 102 from Germany (GER), representing the intensively kept animals and 79 from Switzerland (CH), which were kept extensively, were screened for the presence of different pathogens by PCR, including a new Chlamydiaceae-specific intergenic spacer rRNA gene PCR. Additionally, results of clinical examination and cytology were compared between the symptomatic and asymptomatic pigs of the two groups. Ocular symptomatic pigs showed a high prevalence of Chlamydia suis in both groups: CH 79%, GER 90%. Only 23% asymptomatic pigs from CH, but 88% asymptomatic pigs from GER were positive for C. suis by PCR. DNA of Chlamydia-like organisms were detected in 19% CH, but only in 2% GER pigs, whereas only 4% CH and 1% GER pigs were also positive for Acanthamoebae spp. A co-infection of Acanthamoebae spp. and C. suis was present in only 3% of the CH but 28% of the GER pigs. In general, the intensively kept pigs in our study seemed to be pre-disposed to ocular chlamydial infection and associated conjunctivitis. Infections with Chlamydia-like organisms alone and in combination with Acanthamoebae played no role for clinical findings within the tested pig groups, whereas a co-infection of Acanthamoebae and C. suis was able to cause serious ocular manifestations in half of the cases of intensively kept pigs being positive for these microorganisms.