The aim of this prospective study was to evaluate the prevalence and pattern of gastrointestinal malformations (GIM) among Iranian newborns in Gorgan, North of Iran. From 1998 through 2003, 37,951 live births in Dezyani hospital in Gorgan, North of Iran, were screened for gastrointestinal malformations. Clinical and demographic factors of diagnosed cases were recorded in a pre-designed questionnaire for analysis; sex, ethnicity, type of GIM and associated anomalies. The overall prevalence rate of gastrointestinal malformations was 10 per 10,000 births. The imperforate anus (5 per 10,000) was the commonest birth defect in gastrointestinal tract. The prevalence rate of GIM was 8.2 per 10,000 in males and 10.7 per 10,000 in females. According to the parental ethnicity, the prevalence rates of GIM were 6.7, 15.8 and 17.6 per 10,000 in Fars, Turkman, and Sistani, respectively. There were eight cases (21%) with associated anomalies. The prevalence rate of GIM in North of Iran is not similar to the previous studies in Iran and Middle East and ethnic background may be a causative factor in the rate of GIM in this area.