Introduction The prognosis of congenital anomalies (CAs) can be improved if detected and treated accurately. Given the complexity of some anomalies, it is almost always necessary to approach them with an interdisciplinary team. Our objective was to contact patients with congenital urological anomalies (CUAs) and follow them up during their first years of life and evaluate their clinical status, as well as their social and health care limitations. Method Based on the Bogota Congenital Malformations Surveillance Program (BCMSP), we have contacted by phone all the patients with CUAs and evaluated their follow-up. We have included all the registered patients from 2006 until 2015. A standardized questionnaire was applied by a trained staff. The questions assessed on each call included: evaluation of the clinical status of the patient, the clinical treatments and evaluations performed by clinical and surgical subspecialties, health care limitations, and social barriers. The first call was made at the 2nd month, then every 3 months during the 1st year and every 6 months thereafter. Results A total of 277 patients were contacted, 97.3% of whom have an increased risk of mortality or significant disability. The malformation related mortality was of 38.1%. Only 38.7% of the patients were evaluated by a specialist, while 57.4% where still waiting to be seen by a specialist. Ninety eight percent of the limitations related to the health care system were the long waiting lists to be seen by a specialist. Conclusion Many of the pathologies that we have found belong to the group that has a significant reduction in mortality when treated accurately and promptly. However, we have a profound problem in our health care system, in that many of the patients have not been seen by a specialist, which results in a worse prognosis and recovery rate.