Abstract Background Cervical screening detects precancerous cells and routine screening could be improved by testing for Human Papillomavirus (HPV), the virus that causes cervical cancer. HPV infection is common and the benefit of HPV testing would be identification of women who are HPV negative and at low risk of developing cancer. Study design The aim of this study was to evaluate the Greiner Bio-one PapilloCheck ® micro-array assay (PapilloCheck) for detection of HPV in comparison with Hybrid Capture II (hc2) and PCR-enzyme immunoassay (PCR-EIA) using the GP5/6+ primers. Results Samples from a cytologically defined population ( n = 878) were analysed and 187 samples also had histology information. Overall, 674 out of 878 samples gave a consistent result (76.8%; 95% CI 73.83–79.52%) on all three platforms. The genotype results obtained by PapilloCheck and PCR-EIA were compared and 94% were consistent (95% CI 92.1–96.4%). The main difference was the poor Kappa agreement for detection of high risk (HR) type 35 (Kappa = 0.190) with all inconsistent results being HR positive by PCR-EIA assay but negative on the PapilloCheck platform. There was no statistically significant difference between the performance of each assay when HR HPV positive samples were linked with clinical result (cytology and histology grade). PapilloCheck detected the highest number of HR HPV infections in samples with histology confirmed as CIN1, CIN2 and CIN 3 (76.6%, 85% and 91.7%, respectively). Conclusions Overall, PapilloCheck proved to be a sensitive, reproducible, robust molecular assay for HPV genotyping with the potential for high throughput of specimens in a clinical setting.