More evidence is needed that links the diagnosis of different congenital heart diseases (CHD) identified after birth, with intermediate altitudes above sea level in geographically and ethnically diverse populations. Our aim was to estimate relative frequencies of CHD diagnosis by altitude and gender in the pediatric population of 12 cities in Colombia. This was a cross-sectional study based on the information collected between 2008 and 2013 in Colombia, during annual congenital heart disease (CHD) case detection campaigns in the post-natal period. All children underwent physical examination, pulse-oximetry, and echocardiography. The odds ratio (OR) was used as the summary statistic to assess associations with altitude in the relative frequency of CHD diagnosis. Data from 5900 children who attended the campaigns were evaluated (54.3 % male), out of which 3309 (56.1 %) were diagnosed with CHD. There were statistically significant differences in the relative distribution of the different CHD by city altitude and gender (p < 0.0001). When compared with sea level, altitudes between 1285 and 3000 m above sea level were associated with increased Patent Ductus Arteriosus (PDA) (ORmh 1.68, 95 % CI 1.34–2.09; p < 0.0001) and left ventricular outflow tract obstruction (LVOTO) diagnoses (ORmh 2.06, 95 % CI 1.63–2.61; p < 0.0001), while the opposite was true for right ventricular outflow tract (RVOTO) diagnosis (OR 0.60; 95 % CI 0.49–0.74, p < 0.0001). These associations were not modified by gender differences. In a geographically and ethnically diverse population, altitudes between 1285 and 3000 m above sea level carried an independent and clinically important excess diagnostic risk of PDA and of LVOTO, when compared to all other CHD.