The objective was to analyze the incidence of congenital syphilis and the factors associated with vertical transmission in the 16th Regional Health System of the State of Paraná. This is a cross-sectional survey conducted by pairing the notifications in the Sinan, Sinasc and SIM databases between 2012 and 2017. The statistical analysis was calculated using absolute and relative frequencies and the Chi-square test, with a 95% confidence level. The incidence of congenital syphilis rose from 0.41/1,000 live births to 6.07/1. 000 and was associated with the diagnosis made in the third trimester of pregnancy (OR= 2.051), treponemic test not performed or ignored in the diagnosis of gestational syphilis (OD=2.339) and titrations of the non treponemic test between 1:8 and 1:16 (OD= 2.386) and between 1:32 and 1:64 (OD= 2.353). The neonatal variable associated with syphilis was a congenital anomaly (p=0.037). It was concluded that it is necessary to improve the assistance regarding early diagnosis, correct treatment and follow-up.