Rationale, Aims, and Objectives Quick diagnosis units, a paradigmatic innovative model of hospital ambulatory medicine in Spain, are suggested to be cost-effective. While former studies have been conducted as cost analyses of single units or comparative analyses between these patients and inpatients hospitalized for the same condition, how cost outcomes compare between units of different hospitals and different levels of complexity is unknown. Using micro-costing, the costs of patients managed at quick diagnosis units from a tertiary and a secondary hospital were compared. Methods The study population included 407 patients from each unit who were evaluated over 8 years. Through a bottom-up approach, we analyzed all single cost components that contributed to the mean total cost per patient in both units. Results Patients from the tertiary hospital unit were more likely than those from the secondary hospital to be referred for cancer suggestive symptoms, to have a diagnosis of cancer, and to be referred from the emergency department. Although the ratio of successive/first visits was 3.098 ± 0.6584 in the tertiary vs. 2.123 ± 0.2171 in the secondary hospital unit (P=0.0064), the time to diagnosis was significantly longer in the latter. With a similar mean cost per visit, the cost per patient was \euro577.5 ± \euro219.6 in the tertiary vs. \euro394.7 ± \euro92.58 in the secondary hospital unit (P=0.0559). Personnel and indirect costs including both the monetary estimate and their percent contribution to the mean cost per patient accounted for the main differences between units. Conclusion The ratio of successive/first visits was the main driver of cost differences. A greater complexity of patients from the unit of the tertiary hospital and the inherent characteristics of this type of hospital including volume of patients and staff and staff time justified the differences in the ratio of visits and the cost outcomes.