Objectives: To identify functionally altered signaling pathways that drive tumorigenesis of invasive cervical cancer through integrated analysis of genomic, transcriptomic, proteomic, and clinical data. Methods: Blood and primary frozen tumor tissue were obtained from untreated women with invasive cervical cancer. Integrated analysis was done from mRNA, whole exome DNA, and miRNA sequencing data, and with DNA methylation and copy number data. A comprehensive core sample set consisted of 178 matched samples with some platform data on an additional 67 cases. Protein data were available in 155 cases. Results: Integrated analysis showed novel molecular features and defined significant cervical cancer subgroups. Key distinguishing features of squamous cell carcinomas include activation of p53, p63, p73, AP-1, MYC, HIF1A, FGFR3, and MAPK signaling, which is similar to features characterizing squamous-like cancers in general. Alterations in RTK, PI3K, and MAPK pathway were observed across both squamous cell carcinomas and adenocarcinomas. Adenocarcinomas harbor more ERBB2, ERBB3, and KRAS alterations compared with squamous carcinomas. A unique set of endometrial-like cervical cancers was identified that was predominantly human papillomavirus (HPV)-negative and had high frequencies of KRAS, ARID1A, and PTEN aberrations. Molecular diversity was observed in squamous cell carcinomas where a subset of cases exhibited an epithelial-mesenchymal transition signature derived from mRNA and protein data with poor overall survival. Several findings underline the importance of the immune system in HPV-related cancers, including mutations in HLA, amplifications in immune targets (PD-L1, PD-L2) and an immune-related mRNA signature significantly associated with survival. Novel findings such as amplifications in the BCAR4lincRNA, associated with estrogen therapy resistance, were also identified. Extensive HPV characterization by Mass Array, and by DNA and RNA sequencing shows the presence of HPV in 95% of cases. Viral-cellular fusion transcripts were observed in 83% of HPV-positive cancers. HPV integration was observed in all HPV18-infected cases and 76% of HPV16-infected cases, with integration sites found in areas that had structural aberrations and associated with increased expression of target genes. Conclusions: These findings provide insight into novel molecular subtypes for targeted therapies for cervical cancer.