Acute leukemia is the most common childhood cancer and has been associated with exposure to environmental carcinogens. This study aimed to identify clusters of acute childhood leukemia (ACL) cases and analyze their relationship with proximity to industrial sources of air pollution in three capital cities in Colombia during 2000–2015. Incident ACL cases were obtained from the population cancer registries for the cities of Bucaramanga, Cali, and Medellín. The inventory of industrial sources of emissions to the air was obtained from the regional environmental authorities and industrial conglomerates were identified. The Kulldorf’s circular scan test was used to detect city clusters and to identify clusters around industrial conglomerates. Multivariable spatial modeling assessed the effect of distance and direction from the industrial conglomerates controlling for socioeconomic status. We identified industrials sectors within a buffer of 1 km around industrial conglomerates related to the ACL clusters. Incidence rates showed geographical heterogeneity with low spatial autocorrelation within cities. The spatio-temporal tests identified one cluster in each city. The industries located within 1 km around the ACL clusters identified in the three cities represent different sectors. Exposure to air pollution from industrial sources might be contributing to the incidence of ACL cases in urban settings in Colombia.