This study examines the spatial structure of children with cleft lip and palate (CLP) and its association with polluted areas in the Monterrey Metropolitan Area (MMA). The Nearest Neighbor Index (NNI) and the Spatial Statistical Scan (SaTScan) determined that the CLP cases are agglomerated in spatial clusters distributed in different areas of the city, some of them grouping up to 12 cases of CLP in a radius of 1.2 km. The application of the interpolation by empirical Bayesian kriging (EBK) and the inverse distance weighted (IDW) method showed that 95% of the cases have a spatial interaction with values of particulate matter (PM10) of more than 50 points. The study also shows that 83% of the cases interacted with around 2000 annual tons of greenhouse gases. This study may contribute to other investigations applying techniques for the identification of environmental and genetic factors possibly associated with congenital malformations and for determining the influence of contaminating substances in the incidence of these diseases, particularly CLP.