The authors examined 130 newborns and nursery children from September 1999 till May 2003 from the Prague district for the surmise of chlamydial conjunctivitis. Chlamydia infections were detected in conjunctival smears. Chlamydia trachomatis was confirmed in 20 (15.3%) using ligase chain reaction and C. pneumoniae in 16 (12.3%) children using an indirect immunofluorescent method. Direct captures of chlamydial infections of newborns were included in the study. The authors had also examined 671 newborns in a maternity hospital from January 2002 till May 2003. Conjunctival scraping had been done in 29 (4.3%) cases mainly for mucopurulent conjunctivitis. Chlamydial conjunctivitis was identified only in 4 (0.6%) cases, i.e. C. trachomatis and C. pneumoniae in 2 cases each. Initial clinical symptoms of both types of chlamydial conjunctivitis were similar (mucous discharge with various degrees of eyelid effusion and chemosis mainly on the tarsal conjunctiva). Clinical symptoms of the C. pneumoniae infection were later accompanied by pseudofollicular changes on the tarsal conjunctiva. The complication of this infection was lacrimal obstruction among half of newborns. Clarithromycin in syrup at a dose of 15 mg/kg/per day for 14 days ensured effective treatment of both chlamydial infections. Control scrapings were always negative and simultaneously the pathological conjunctival finding disappeared.