To compare Fourier-transform infrared (FTIR) spectroscopy in screening cervical cytology and standard Papanicolaou (Pap) screening with colposcopic directed biopsy as a "gold standard," we prospectively gathered FTIR samples and Pap smears of all patients attending our program's colposcopy clinics, from February to October 1995. We recorded demographic data for each patient including colposcopy, cytology, treatment follow-up, and histology. Using the colposcopically directed biopsy as the gold standard, exfoliated cervical cells from 301 patients were collected to compare cytology and FTIR spectroscopy. Based on previously established criteria, we provided distinctive definitions of both negative/positive FTIR, cytology, and histology. Results of 301 cases showed 196 positive and 105 negative cytologies. The sensitivity, specificity, false-negative rate, and false-positive rate for the Pap test were 86.6, 90.5, 13.4, and 9.5%, respectively. However, FTIR results versus histology showed 215 positive and 86 negative with a sensitivity of 98.6% and specificity of 98.8%. False-negative and false-positive rates were 1.4 and 1.2%, respectively. In the 12 cervical cancers there were no false-negative FTIR results but 3 false-negative Pap smears. The positive and negative predictive values for FTIR were 99.5 and 96.5% while the Pap values were 95.9 and 72.3%. Compared to standard Pap smears, FTIR has a better false-negative rate and negative predictive value in this preliminary study. Further work, to establish the range of each of the spectral criteria for different grades of dysplasia and that among various infectious effects, needs to be conducted before applying this research tool to a population-based study.