The use of waste materials in nature (e.g. fly ash, bottom ash) in the construction phase of buildings is of great importance both in terms of environmental pollution and the construction cost of the structures. Therefore, in this study, the effects of bottom ash and fly ash on the construction cost of reinforced concrete (RC) hospital buildings are investigated by considering experimental tests and 3D nonlinear analyzes. During the experiments, four different concrete series are created and fly ash and bottom ash are added to replace 0–5 mm grain size aggregates in the concrete mixture at different ratios. The RC beams created according to four different concrete series are subjected to experimental tests. Afterward, it is determined that the most critical mixing ratio for RC beams subjected to experimental tests is selected as 75% bottom ash ratio and fly ash. For the purpose Ankara Bilkent City Hospital is selected for 3D nonlinear seismic analyses and the hospital structure is subjected to 10 various earthquake analyses. This study showed that there was a noticeable decrease in the construction cost when the costs of the hospital structure were compared as a result of the earthquake analysis. Another important point is that the use of bottom ash and fly ash is thought to contribute to savings in the energy to be used for the storage of wastes by causing less electrical energy use in cement production, less greenhouse gas emissions, natural raw material consumption and nature pollution.