BACKGROUND Hypospadias is one of the most common congenital anomalies in male infants, defined as incomplete development of the urethra. Despite the wealth of literature, there are conflicting data on the values and trends of prevalence, due to multifactorial origin but often also to methodological differences between studies. The aim of this study was to analyse prevalence, trends and risk factors of hypospadias in the Emilia Romagna Region, Italy. METHODS The Emilia-Romagna Registry (IMER) is a population-based congenital anomaly database covering the first year of life, active since 1978. IMER uses multi-source ascertainment, including hospital discharge records (SDO) from 2009, through a validated algorithm. From 2014, IMER changed the algorithm, and included all hypospadias identified in SDO, and not only those confirmed by surgery. All cases identified in the IMER database, coded 7526.01-7526.09 or Q54.0-Q54.9 in 2010-2016, were analysed. CONCLUSIONS A total of 604 hypospadias cases were registered among 267,285 births; 526 were isolated, giving a prevalence of 2 per 1000. An increase from 1.6 in 2010 to 2.9 in 2016 was seen. The comparison between consecutive years was not significant neither from 2010 to 2013 nor in the period 2014-2016. There was instead a significant difference between the two periods, suggesting that the ascertainment change in 2014 is probably responsible for the increase. In the last three years analysed, isolated hypospadias prevalence is 2.5 per 1000. In the study period, mother's age over 39 years, multiple birth, preterm birth, small for gestational age, Caucasian compared with Asiatic or Africans were statistically associated with higher hypospadias prevalence. There was no association neither between hypospadias and paternal age nor maternal body mass index or assisted reproductive technology. CONCLUSIONS Whilst hypospadias prevalence trend is debated in the literature, in IMER it seems to be stable, with methodological changes affecting the trends. Risk factors potentially involved in developing hypospadias are environment and population characteristics, so understanding and monitoring hypospadias prevalence remains important.