Abstract: Systems and methods for automated screening of cervical and endocervical epithelium for malignant and premalignant lesions comprise collecting the epithelial cell sample in a transport fluid medium. Cells suspended in such medium are analyzed by flow cytometric technology. DNA fluorescent in-situ hybridization technology is also used to identify human papilloma virus (HPV) infected cells by means of flow cytometry. Different cell populations are quantitated as part of a complete cell count (CCC). CCC data is correlated with HPV DNA in-situ hybridization results. CCC data and CCC/HPV DNA in-situ hybridization correlation results are displayed both in three dimensional graphical form as well as two dimensional dot plot graphs depicting specific gated cellular populations. Populations of interest can also be sorted for subsequent visual morphologic inspection as well as for molecular diagnostic studies.