This paper deals with the seismic response of the soil underneath a school in Catania (Italy), characterized by a high seismic hazard. Studies of the seismic soil response by 1D analyses are carried out according two different levels of knowledge proposed for the soil: i) a limited level (LC1) acquired by initial design information; ii) an adequate level (LC2) acquired by recent geotechnical investigations. Each knowledge level is characterized by a proposed geotechnical confidence factor. Italian Regulations propose knowledge levels and confidence factors for structures, but ignore theme for soil and foundations. Seven different accelerograms, scaled at the same PHA with reference to the estimated seismicity of Catania, are applied at the bedrock. Soil nonlinearity is taken into account according to Eurocode 8. The dynamic response of the system is analysed in the time and frequency domains. The main goal of the paper is to stress the importance of the different geotechnical knowledge levels in the evaluation of the design/retrofitting seismic inputs in terms of acceleration time histories, amplification factors, response spectra and amplification function. The application of the proposed procedure is a useful methodological example for the designers.