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To explore the level and feature of neonate deformity in water arsenic exposure areas, as to finding out an evidence for the study and prevention of the arsenic exposure.The birth situation of neonate was surveyed from 1998 to 2004 in water arsenic exposure areas according to cross-sectional survey. The results were classified in accordance with ICD-10 and common surveillance of china. The population of Shanyin County served as the common people and the data were analyzed by SPSS 11.5 for windows.The neonates surveyed were 2467 cases. There were 49 neonates deformity found in this investigation, giving a neonate deformity rate of 198.62 per 10,000 cases, which was shown significantly higher in water arsenic exposure areas than in the normal (U = 3.23, P0.01), with types of nervous system deformity, limbs deformity and congenital heart disease as in system classification. There was no significant difference of deformity rate in different sex neonates (chi2 = 0.32, P0.05).The drinking high-arsenic water over a long period of time should be a risk factor of neonate deformity. Prevention and treatment of endemic arsenic exposure should be urgently needed.