This paper proposes an innovative and transparent methodology to support the "ASL Milano" (Local Health Agency) in the hygiene and health evaluation of construction projects, in order to highlight their positive and negative performance beyond the requirements imposed by the current laws and regulations regarding buildings' hygiene performance, which are too old and therefore unsuitable to ascertain the real quality of indoor environments. The compliance with laws or regulations, mostly out of date, and the assessment of performance involving only a part of the current emerging needs and problems, in fact, should be considered as a necessary, although not a sufficient step, to ensure high quality indoors. Consequently, it is necessary to identify and test an assessment tool which could provide an effective and flexible support for the development of hygiene and health statements regarding projects at building scale (new construction, conversion of the existing, rehabilitation, extension, change of use, etc). The assessment tool suggested by this paper is tailored for the metropolitan area of the city of Milan, but its evaluation framework could be developed and applied to other contexts.