The catalytic subunit alpha of phosphatidylinositol 3-kinase (PIK3CA) has been expected to play a role as an important oncogene in uterine cervical carcinoma, whose expression in non-invasive lesions has received considerable attention. We investigated the potential of PIK3CA as a carcinogenesis-related marker for early intraepithelial lesion of the uterine cervix in cytology samples. Seventy-four cases with abnormal cytology suggesting the existence of cervical intraepithelial neoplasia (CIN) lesions, whose findings were histologically confirmed, were selected; they consisted of 20 CIN1, 21 CIN2, and 33 CIN3, respectively. In addition, 17 normal cases, whose cervical cytology revealed no abnormality over three occasions, were selected. Liquid-based cytology specimens were applied for human papillomavirus (HPV) DNA typing and immunocytochemistry using three different antibodies for p16(INK4a), Ki-67 and PIK3CA, respectively. The fraction of immunopositive cells on the slides was calculated and expressed as mean numbers. Receiver operating characteristic (ROC) plots were generated to determine the diagnostic accuracy of each immunocytochemistry test. The mean number of immunopositive cells in the CIN3 group was significantly higher than other groups for all three antibodies. Among all groups, PIK3CA showed a superior specificity to distinguish CIN3 from other groups. Comparison of three markers by ROC curves also revealed that PIK3CA provided the best method for distinguishing CIN3. Thus, expression of PIK3CA was observed in liquid-based cytology in CIN lesions, which suggested its diagnostic significance in addition to the use of routine cervical cancer smear and the HPV screening program.