The “gold standard” for diagnosis of C. trachomatis infections in infants and children remains isolation by culture of C. trachomatis from the conjunctiva, nasopharynx, vagina, or rectum. C. trachomatis culture has been defined further by the Centers for Disease Control and Prevention (CDC) as isolation of the organism in tissue culture and confirmation by microscopic identification of the characteristic inclusions, preferably by staining with a fluorescein-conjugated species-specific monoclonal antibody.4 Several nonculture tests are approved for diagnosis of chlamydial conjunctivitis in infants, specifically enzyme immunoassays (EIAs), and direct fluorescent-antibody tests (DFAs). The only EIA and DFA assays still available in the United States are Pathfinder® Chlamydia DFA and EIA Microplate (Bio-Rad Laboratories). These tests appear to perform well with conjunctival specimens with sensitivities 90% or more and specificities 95% or more compared with culture.3 There are currently three FDA-approved, commercially available NAATs for diagnosis of C. trachomatis infection: PCR (Amplicor, Roche Molecular Diagnostics, Nutley, NJ), strand displacement amplification (ProbeTec, Becton Dickson, Sparks, MD), and transcription-mediated amplification (GenProbe, San Diego, CA). These assays all have FDA approval for cervical swabs from women, urethral swabs from men, and urine from men and women.4 Data suggest that PCR is equivalent to culture for detection of C. trachomatis in the conjunctiva and nasopharynx of infants with conjunctivitis; however, PCR and other NAATs do not have FDA approval for use with conjunctival specimens.23 The identification of C. trachomatis and/or N. gonorrhoeae in a newborn infant indicates untreated infection in the parents.