Evaluation of Human Papillomavirus (HPV) testing systems suitable for large-scale organized cervical screening programs is required. We evaluated the cobas 6800 HPV test system for detection of cervical intraepithelial neoplasia grade 3 or worse (CIN3+) when nested in an organized primary HPV screening program, using the cobas 4800 test as comparator. The Karolinska University Hospital Cervical Cytology Biobank, containing frozen cervical samples from >700,000 women participating in organized cervical screening, was linked to the Swedish national cervical screening registry to identify 470 stored cervical samples taken <180 days before histopathological diagnosis of CIN3+. Two controls per case, with no abnormal results for 2 screening rounds, matched for age and sampling time were also retrieved. Aliquots from 1406 women were retrieved and re-tested on the cobas 4800 system and tested on the cobas 6800 system. There was high reproducibility between the original cobas 4800 HPV test results, and the cobas 4800 HPV re-testing performed on the samples retrieved from biobank storage. 462/464 biobanked samples from women with CIN3+ tested HPV-positive on the cobas 6800 system, corresponding to a relative sensitivity of 99.6%. 925/932 biobanked samples from control women tested HPV-negative on the cobas 6800 platform, corresponding to a relative specificity of 99.2%. By conventional criteria, the cobas 6800 was non-inferior both regarding relative sensitivity of >90% (non-inferiority p-value <0.0001) and relative specificity of >98% (non-inferiority p-value 0.006). We conclude that the cobas 6800 HPV test system had similar, high performance as the cobas 4800 such, when evaluated using cervical samples taken before CIN3+ in a real-life primary HPV screening program.