The distribution and prevalence of 33 high-, medium-, and low-risk HPV genotypes were surveyed in women aged between 15 and 54 years and with normal cytology in the biggest cities and regions in Bulgaria (viz., Sofia, Plovdiv, Varna, and Burgas) and in two smaller communities (viz., Pleven and Vidin). This survey was also intended to update previous data collected in 2012 and to assess the results of a national campaign to immunize all 12-year-old girls against HPV, which was also started in 2012. The GenoFlow HPV Array Test Kit was used to analyze HPV status in cervical samples collected in 2012-2016 from 5277 women who had visited 47 gynecological clinics across the study sites. HPV infection was confirmed in 1570 (29.8%). The most common infecting genotype was HPV-16, which was detected in 687 women (13%), followed by HPV-56 in 333 women (6.3%), HPV-33 in 209 cases (4%), and HPV-31 in 190 subjects (3.6%). This is the second study to assess the prevalence of HPV infection in larger Bulgarian cities including the capital and to draw attention to the unusually high proportion of specific infecting genotypes.