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Many studies show that congenital defects in infants conceived by assisted reproductive techniques (ART) are more than infants of normal conception (NC). The aim of this study is to determine the frequency of congenital anomalies in ART infants from Royan Institute and to compare congenital anomalies between two ART techniques. In a cross-sectional descriptive study, 400 ART infants from Royan Institute who resided in Tehran were selected by non-random, consecutive sampling. Infants were examined twice (until 9 months of age) by a pediatrician. Infants' congenital anomalies were described by each body system or organ and type of ART. Data were analyzed by SPSS version 16 and Fisher's exact test.The frequency of different organ involvement in the two examinations were: 40 (10%) skin, 25 (6.2%) urogenital system, 21 (5.2%) gastrointestinal tract, 13 (3.2%) visual, and 8 (2%) cardiovascular system. Major congenital defects in infants conceived by in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) were hypospadiasis, inguinal hernia, patent ductus arteriosus plus ventricular septal defect (PDA + VSD), developmental dysplasia of the hip, lacrimal duct stenosis during the first year of life, hydronephrosis and urinary reflux over grade III, undescending testis, ureteropelvic junction stenosis, and torticoli.Two-thirds of ART infants had no defects. A total of 7% of IVF and ICSI infants had one of the major abovementioned congenital anomalies. This rate was higher than NC infants (2%-3%). There was no difference between the ICSI and IVF group.