Chlamydia trachomatis is a frequent sexually transmitted disease. The diagnosis of C. trachomatis infection by cytology is controversial. We compared the ability of Papanicolaou (Pap) smears to detect C. trachomatis infection with antigen detection (enzyme immunoassay; EIA) and polymerase chain reaction (PCR). One hundred sixty-seven women attending a therapeutic abortion clinic were enrolled in the study. Endocervical samples were first collected for EIA and PCR, and then Pap smears were prepared for cytologic evaluation. Eight patients were excluded from the study due to the lack of an endocervical component. The criteria established by Gupta and associates (Diagn Cytopathol 1988;4:224-229; Acta Cytol 1979;23:315-320) were used in this study to assess the specificity and sensitivity of the Pap smear in recognizing C. trachomatis infection. After EIA testing, the remaining sample was subjected to phenol-chloroform extraction to purify the DNA and then tested by PCR. Positive PCR samples were subjected to repeat phenol-chloroform and retested to confirm the positive result. Using a confirmed PCR or a blocked EIA as the extended gold standard, the incidence of C. trachomatis infection was 9.4%. Fifteen of the 159 cases reviewed were positive by extended gold standard. Thirteen (86.7%) of those 15 cases were interpreted as negative by cytology (false-negatives), and two (13.3%) cases were positive. Of the remaining 144 cases, 14 cases (9.7%) were interpreted as positive by cytology (false-positives) but were not confirmed by the extended gold standard. Ten (66.7%) of the 15 cases confirmed by the extended gold standard were interpreted as negative by EIA (false-negatives), and five (33.3%) were positive. There were no false-positives by EIA. In this study, the sensitivity and the specificity for cytology were 13.3% and 90.3%, respectively. The positive predictive value was 12.5%, and the negative predictive value for cytology was 90.9%. The sensitivity and the specificity for EIA were 33.3% and 100%, respectively. The positive predictive value was 100%, and the negative predictive value for EIA was 93.5%. Both EIA and cytology are insensitive methods compared with PCR. Based on these data, cytology should not be used to diagnose C. trachomatis infection in an asymptomatic female population with a moderate risk of C. trachomatis infection.