Cervical intraepithelial neoplasia grade 3+ (CIN3+) and adenocarcinoma in situ incidence will be an important measure of HPV vaccine impact. Integrated healthcare delivery systems, such as Kaiser Permanente, could be used to monitor CIN3+ trends; however, limited evaluations of data from healthcare delivery systems for CIN3+ surveillance exist. We compared CIN3+ diagnoses by ICD-9 code with CIN3+ diagnoses by pathology results among 121,211 females aged 11 to 30 years who were continuously enrolled from 2000 to 2005 in either Kaiser Permanente Northern California or Kaiser Permanente Northwest. We calculated sensitivity and positive predictive value of diagnosis by ICD-9 codes using pathology CIN3+ diagnosis as the gold standard. There were 1,090 women with at least one CIN3+ diagnosis by ICD-9 code 233.1 and 1,200 women with at least one CIN3+ diagnosis by pathology results. The sensitivity of the ICD-9 code for detecting a woman with at least one pathology diagnosis for CIN3+ was 62% (740/1,200); positive predictive value was 68% (740/1,090). Among women with at least one CIN3+ diagnosis by ICD-9 code, 679 (62%) had more than one visit with this code; whereas, among women with at least one CIN3+ diagnosis by pathology, 466 (39%) had more than one CIN3+ pathology result. ICD-9 codes may underestimate the number of women with at least one CIN3+ diagnosis. Pathology results, when available, may provide better estimates of CIN3+ incidence.