OBJECTIVE: To evaluate whether ThinPrep smears without versus those with a transformation zone component were more likely to have falsely negative cytology findings. METHODS: Women aged 18–50 ( N = 4389) attended one of three Planned Parenthood clinics between 1997 and 2001 for screening by ThinPrep Papanicolaou and polymerase chain reaction-based human papillomavirus (HPV) DNA testing. Women with 1) any cytologic abnormality, 2) high-risk HPV types, and 3) a random sample with normal Papanicolaou and negative HPV tests were offered repeat cytology, colposcopy, and biopsy. Cytology and biopsy diagnoses at the colposcopy visit were reviewed according to the presence ( n = 3689) or absence ( n = 700) of a transformation zone component at screening. RESULTS: Among women with normal cytology at screening, histologic detection of at least cervical intraepithelial neoplasia grade 2 (odds ratio 1.3, 95% confidence interval 0.5, 3.3) at colposcopy did not differ significantly between transformation zone-positive and zone-negative smears. Histologically confirmed cervical intraepithelial neoplasia grade 1 was detected more often among smears lacking a transformation zone component (odds ratio 2.0, confidence interval 1.0, 3.8). Transformation zone-negative smears were more common among older women, current oral contraceptive users, those past the 14th day of their last menstrual period, and those negative for high-risk HPV types. CONCLUSION: Absence of a transformation zone component in a screening ThinPrep Papanicolaou test was not associated with missed high-grade lesions. Based upon our data, we do not recommend repeat screening of reproductive-aged women with negative liquid-based tests and no cytologic evidence of a transformation zone component.