The E1 and E2 reading frames of 158 cervical carcinoma samples containing human papillomavirus (HPV) 16 were mapped using polymerase chain reaction (PCR). The reading frames were amplified using primers spanning the entire genes. Of the analyzed samples, 23% showed no amplification with the E1 primers and 29% showed no amplification with the E2 primers. There was an overlap, but not complete identity, between the E1− and E2-disrupted groups. All E1− and E2-negative samples were further analyzed with primers spanning subsections of the E1 and E2 reading frames, which together covered the entire genes. Of the 35 samples negative for EI, 11 were positive in specific amplification of the 3′ end of the E1 gene. Several different subsections of E2 could be amplified from most samples negative for the entire gene (37/46). Five classes of patterns were found, in which either all subsections of the E2 gene or subsections in the 5′, middle, or 3′ end were disrupted. Although a variable pattern of disruption/deletion in the E1-E2 area of the HPV 16 genome was found in cervical carcinoma, the 5′ end disruption was the most common one in both E1 and E2. Patients with carcinomas showing disruptions in E1/E2 had a poorer survival than those without such changes, and E1 disruptions were the most important prognostically.