Background and aims Congenital malformations (CM) are defined as abnormal structure of the organism resulting from disrupted embryogenesis. Many factors influence the appearance of CM. Regarding different criteria and authors, the incidence of CM at newborns is between 2–7%. The aim of this paper was to determine the incidence of CM at liveborns delivered at SHGO “Mother Teresa” – Cair, Skopje, during the five years period (2000–2004) and five years period (2005–2009). Also, the distribution among organ system had been analysed.

Methods A retrospective analysis of 19097 liveborns delivered at SHGO Cair, during 2000–2004, has been performed. Database (Access 2000) from Neonatal Unit has been used. The incidence and percentage of CM among different systems have been determined and a retrospective analysis of 15293 liveborns delivered at SHGO Cair, during 2005–2009, has been performed. Database (Access 2005) from Neonatal Unit has been used. The incidence and percentage of CM among different systems have been determined.

Results Period 2000–2004, among a total of 19097 liveborns, 736 or 3,85% have had CM. the incidence between different years was:4,28% in 2000, 3,92%-2001, 3,79%- 2002, 3,20%-2003 and 3,98% in 2004. Regarding different organ systems the distibution was: 58,1% of all CM were the anomalies of musceulosceletal system, 14,6% – cardiopathies, 8,1% - anomalies of uro-genital system 7,2% -CM of gastro –intestinal system, etc. Perid 2005–2009, among a total of 15293 liveborns, 573 or 3,75% have had CM. the incidence between different years was:4,02% in 2005, 3,42%-2006, 3,22%- 2007, 4,23%-2008 and 3,85% in 2009. Regarding different organ systems the distibution was: 40,31% of all CM were the anomalies of musceulosceletal system, 21,81% - cardiopathies, 20,07% - anomalies of uro-genital system, 12,04% -CM of gastro –intestinal system, 5,76% of CNS, etc.

Conclusions During the five years period (2000–2004), the incidence of CM is 3,85%, which is in accordance with data from literature. Among years, the incidence varies from 3,2 to 4,3%. During the five years period 2005–2009, the incidence of CM is 3,75%, which is in accordance with data from literature. Among years, the incidence varies from 3,2 to 4,3%. The anomalies of musculoskeletal system are the most frequent, followed by those from cardiovascular, uro-genital, gastro-intestinal and central nervous system. Comparing the five-year periods 2000–2004 and 2005–2009 shows almost identical incidence. Congenital malformations still remain an important medical and social problem requesting more serious nationwide engagement, as in medical aspect, socioeconomic, ecological, etc.