To establish the frequency of imperforate anus (IA) in the population with Down syndrome (DS) and study the associated risk factors.An observational clinical study case control type was performed. The patients were evaluated at the Unit of Medical Genetics, University of the Andes, from February 2006 to February 2011. The patients with DS and IA were compared with 20 DS without IA. Antecedents of parents were obtained.The frequency de IA in the population with DS was 4.79%. The presence of fever in the first trimester of gestation and the rural origin were associated as risk factors of AI in patients with DS [OR: 25.33 (IC 95% 2.07- 310.76; P = 0.009) and OR: 7.50 (IC 95% 1.09 - 51.52; P = 0.043), respectively]. The maternal age superior to 35 years presented a marginal significance (P = 0.048).These papers emphasize the high frequency of IA in patients with DS and recommend to investigate the prenatal and environmental risk factors that can increase the presence of this anorectal anomaly in the population with DS, in order to consider them in the programs of prevention of congenital pathologies.