Waste landfills are a potential hazard to health. Public concern exists about this potential hazard and researchers agree that further research is required on this field. The objective of the study was to investigate the association between waste landfill location and congenital anomalies risk in Denmark. The study was a multisided epidemiological geographical comparison study of risk of congenital anomalies combined and congenital anomalies of the cardiovascular and nervous systems with maternal residence in the vicinity of 48 Danish waste landfills compared with those living further away in the years 1997 to 2001. We used routine health and population data in Geographical Information System (GIS) to investigate the risk. The subjects were 2,477 live birth with congenital anomalies. All relative risks in the proximal zones of 0-2 km were set to 1 for comparison. For all anomalies combined relative risk in the middle zones of 2-4 km joint was 0.991 and in the distal zones of 4-6 km joint the relative risk was 1.013. For congenital anomalies of the nervous system, the relative risk in the middle zones was 1.226 and in the distal zones 1.113. For congenital anomalies of the cardiovascular system, the relative risk in the middle zones was 0.926 and in the distal zones 0.854. This result was not supported by the aggregated risk ratio mean. We found no association between waste landfill location and congenital anomalies combined or of the nervous system. However, we found small excess risk for congenital anomalies of the cardiovascular system. No causal mechanisms are available to explain these findings, but alternative explanations include approximated birth rates and residual confounding. It is our recommendation that more comprehensive multisided studies will be executed to examine the safety of waste landfills.