The data presented in this article is part in essence of a more extensive dataset aimed at evaluating patterns of change in the temperature-mortality relationship on population health in the city of Valencia, Spain on population health in the city of Valencia, Spain. The complete dataset was used in the framework of the European multi-city project PHASE (Public Health Adaptation Strategies to Extreme weather events) [1]. The data includes daily counts of all-cause mortality, excluding external causes and cardiovascular and respiratory diseases. All-cause mortality is also classified by gender and age groups. Besides temperature, we included other meteorological variables and air pollutants from the PHASE dataset, as well as influenza epidemics. The variable Saharan dust events was also added. All these data were collected from public Governmental data repositories accessible under request. The dataset of this article provides a basis for comparison with similar models for time-series regression, allowing researchers to integrate additional model components without duplication of effort.