Italy is severely affected by floods, yet the government has still to develop a flood risk management strategy that is able to adequately protect the population from the huge financial, human and welfare losses they cause. In this respect, a major obstacle is the limited understanding of risk at the national level. To date, there are no analyses in the literature that estimate the flood losses for the whole Italian territory at the small area level. This is particularly due to the lack of uniformity in the collection of data by the river basin authorities, which are primarily responsible for collecting information on floods in the country. In this work, we combine different sources of flood data and propose a model for flood loss estimation that allows us to predict expected losses per square meter, per municipality, and per structural typology. We identify the areas that are critical to risk management either because of high inhabited density or because of the structural fragility of the assets. Flood expected losses are then compared with those generated by earthquakes, which constitute the natural hazard of main concern in Italy. We find that, in contrast with earthquakes, floods affect only some municipalities. Nevertheless, floods might generate losses per square meter even higher than earthquakes.