Compositions and methods for diagnosing cervical disease are provided. The methods include measuring the expression level of a high-risk HPV E6 and/or E7 RNA in a body sample from a subject, wherein the level of HPV E6 and/or E7 mRNA positively correlates with cervical disease progression. Threshold expression levels of HPV E6 and E7 mRNA are further provided that distinguish normal cervical samples from diseased cells or tissue and samples that are indicative of low-grade cervical disease from those that are indicative of high-grade disease. Further, genes with expression levels that are relatively invariant between normal and various cervical disease states have been identified. Such genes can serve as suitable endogenous controls for the normalization of target gene expression levels in cervical samples. Kits comprising reagents for practicing the methods of the invention are further provided.
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