Vaccination coverage in Ecuador has decreased since 2013, falling short of the World Health Organization’s vaccination goal. There are several causes for this deficiency in coverage, one of these are lost vaccination opportunities, which are caused when a patient without contraindications postpones, or for other reasons fails to receive a recommended immunization. The objective of this study was to determine the state of knowledge regarding vaccination contraindications among the Metropolitan District of Quito health personnel to assess missed vaccination opportunities. Through this cross-sectional descriptive study, health personnel were surveyed online and asked 18 clinical scenarios which were created to evaluate their knowledge of the true contraindications of vaccination, and measure missed opportunities. A total of 273 surveys were collected; 74% belonged to the public health system, and the rest represented by private practitioners. Of those surveyed, 98.2% of health personnel had improperly denied vaccination at least once. We specifically found vaccinations were incorrectly denied more frequently in cases where the hypothetical patient presented mild or moderate fever cases. The use of corticosteroids, autoimmune diseases, and egg allergy were also incorrectly denied (89%, 71.4%, 72.9%, and 58.6%, respectively). Among the health personnel surveyed, there is an apparent lack of knowledge of the true contraindications of vaccination and differences in knowledge about contraindications according to personnel in charge of administering immunization to children. Our preliminary results suggest that lack of education related to side effects could be biasing medical professionals’ decisions, causing them to unnecessarily delay or deny vaccinations, which likely contributes to explaining low overall vaccination coverage in Quito, the capital city of Ecuador.