Background: Anencephaly is a neural tube defect incompatible with life. The aim of this prospective study was to determine the prevalence of anencephaly in Gorgan, northern Iran.Patients and Methods: During 1998 – 2005, 49,534 newborns at Dezyani hospital in Gorgan were screened for neural tube defects. Clinical and demographic data of the diagnosed cases were recorded in a pre-designed questionnaire for analysis. These data included sex, ethnicity, parental consanguinity, and residential area.Results: The overall prevalence of neural tube defects and anencephaly were 28 and 12 per 10000 births, respectively. The prevalence of anencephaly was 11 and 12 per 10000 births in male and female newborns, respectively. Considering the parental ethnicity, the prevalence of anencephaly was 12, 16, and 7 per 10000 in Fars, Turkman, and Sistani ethnicity, respectively. The prevalence of anencephaly was 13.1/10000 in newborns with mothers aged >35 years. Consanguinity was seen in 36% of the parents. The highest rate of anencephaly occurred in 1999 (23/10000) and the least was in 2003 (2/10000). The most prevalent season for the occurrence of anencephaly was winter (16/10000).Conclusion: The present study indicated that the prevalence of anencephaly among Iranian newborns in northern Iran was higher than in the European population.