Background: Atypical glandular cells (AGC) in cervical screening may signal a wide range of conditions from reactive changes to malignancies in the cervix. Atypical cells of unknown origin (AUO) is a rare cytological finding in the Swedish cervical screening program which currently is referred to colposcopy. We set out to investigate the epidemiological evidence for AGC and AUO to be treated as high grade findings that should prompt a direct referral to colposcopy and endocervical evaluation and sampling. Methods: A population-based cohort study was defined as all Swedish resident women who had AGC and AUO findings, respectively, in cervical screening program from 1969 to 2011, retrieved from the National Quality Register for cervical Cancer prevention. Information on subsequent cervical cancer between 1969 and 2011 was obtained from the National Cancer Register. Prevalent cancers and long-term cancer risks after AGC and AUO diagnoses, respectively, were examined, and compared with low-grade and high-grade squamous intraepithelial lesions (LSIL and HSIL). Risk ratios (RR) and hazard ratios (HR) with 95% confidence intervals (CI) were calculated as effect measures. Results: 20,041 women diagnosed with AGC, and 33,253 women diagnosed with AUO, in Pap smear without any other abnormalities before were identified. Among these, 262 were diagnosed with invasive cervical cancer within half a year after AGC (1.31%), and 303 within half a year after AUO (0.91%), which implies possibly prevalent cancers. RR compared to LSIL was for AGC 6.83 (CI=5.92, 7.88), and for AUO 4.76 (CI=4.16, 5.46). RR compared to HSIL was 0.53 (CI=0.47, 0.60) for AGC and 0.37 (CI=0.33, 0.41) for AUO. HR half a year after AGC was 1.91 (CI=1.64, 2.23), compared to LSIL, and 1.32 (CI=1.12, 1.55), compared to HSIL. Correspondingly for AUO, HR=1.67 (CI=1.46), compared to LSIL, and HR=1.15 (CI=1.01, 1.33), compared to HSIL. Conclusions: Both AGC and AUO implies high risk of prevalent or long-term invasive cervical cancer, which warrants direct diagnostic measures and close follow up to find precursors or early carcinomas in the endocervix. We are currently exploring the possibility of increased risk also for endometrial cancer.