Background At present, the HPV DNA test is used to triage young female patients with abnormal cytology. Still, it is not suitable to precisely identify the population with persistent HPV infection. The purpose of this study was to evaluate the diagnostic value of HPV E6/E7 mRNA test in young women with abnormal cytology by comparing HPV DNA test.Methods A total of 258 young women aged 20 to 29 years,with squamous cell abnormalities on the cervical cytology, were enrolled in this study between January 2015 and December 2019.All patients were subject to HPV DNA test, HPV E6/E7mRNA test,colposcopy biopsy, and histopathological examination.A comparative analysis of the diagnostic performance of the HPV DNA test and HPV E6/E7mRNA test was conducted according to the histological diagnosis(CIN II and CIN II+were defined as high-grade squamous intraepithelial lesion+(HSIL+)).Results The results showed that HPV E6/E7 mRNA test had a higher specificity of 47.3%(40.0%-55.1%) for HSIL+ compared to HPV DNA test that had specificity of 16.0% (11.0%-22.6%)in young women(P<0.01). The HPV E6/E7 mRNA test presented high rates of specificity,positive predictive value (PPV), and negative predictive value(NPV), which were 92.1%(86.0%-96.0%), 62.1%(42.4%-78.7%), 92.1%(85.9%-95.8%), respectively, compared to that of HPV DNA,which were 15.8%(10.4%-23.2%),14.6%(9.40%-21.9%), and 71.0%(51.8%-85.1%),respectively(P<0.01)in young women with mildly abnormal cytology(ASC-US and LSIL). Yet, with severe abnormal cytology(ASC-H and HSIL), HR-HPV test was similar to HPV E6/E7 mRNA test in sensitivity(χ2=0.98,P=0.322),specificity(χ2=0.938,P=0.333),PPV(χ2=0.074,P=0.786) and NPV(χ2=0.00,P=1.000).Conclusions Compared to the HPV DNA test,the HPV E6 /E7mRNA test has better clinical value in screening cervical cancer and predicting the risk of HSIL+ in young women, especially those with mild abnormal cytology.