Objective Given the demonstrated utility of human papilloma virus DNA triage in the management of atypical squamous cells of undetermined significance, this study sought to evaluate the potential role of human papilloma virus DNA testing in the evaluation and management of cytological atypical glandular cells. Study design Following institutional review board approval, 28 women presenting with cytological atypical glandular cells underwent repeat thin-prep cytology, Hybrid Capture 2 human papilloma virus DNA testing, colposcopic evaluation, Fisher electrosurgical conization, and endometrial sampling. Human papilloma virus test results in each patient were then correlated with histologic lesions, if present. Results Sixteen of the 28 study patients had pathologic lesions (11/28 high-grade squamous intraepithelial lesion, 3/28 low-grade squamous intraepithelial lesion, 1/28 adenocarcinoma in situ, 1/28 simple endometrial hyperplasia). Human papilloma virus DNA testing was available in 24 of 28 subjects (86%). The sensitivity of human papilloma virus positivity to predict the presence of cervical intraepithelial neoplasia was 100% (confidence interval 77% to 100%), specificity 64% (confidence interval 35% to 85%), positive predictive value 76%, and negative predictive value 100%. Women who tested human papilloma virus positive were 12 times more likely to have cervical intraepithelial neoplasia than women who were human papilloma virus negative (Fisher P<.001). Human papilloma virus positivity was not predictive of endometrial pathology; women who were human papilloma virus positive were less likely to have endometrial pathology than were women who were human papilloma virus negative (risk ratio 1.6, 95% confidence interval 0.01-1.7). Conclusion Atypical glandular cells can represent a variety of lesions. The majority of the lesions will be squamous intraepithelial lesions of the cervix (50%), with high-grade squamous intraepithelial lesion present in 40% of subjects. Human papilloma virus DNA testing is a sensitive test for the presence of squamous intraepithelial lesion, with excellent negative predictive value for the absence of squamous intraepithelial lesion. The results of this study suggest human papilloma virus DNA testing might be an effective screening test in the initial evaluation and management of cytological atypical glandular cells.