Aerogels have recently started to be considered as “advanced materials”; therefore, as a general consideration, aerogels’ toxicity testing should focus on their functionality which resides in their nanoscale open internal porosity. To assess the hazards of organic aerogels, testing at three levels may characterize their biophysical, in vitro and in vivo toxicity, defining distinct categories of aerogels. At the first level of testing, their abiotic characteristics are investigated, and the best aerogel(s) is forwarded to be tested at level 2, wherein in vitro methodologies may mainly evaluate the aerogels’ cellular behavior. Within level 2 of testing, the main characteristics of toxicity are investigated and the selected aerogels are introduced to in vivo animal models at level 3. In the animal model testing, target organs are investigated along with systemic parameters of toxicity. Some study cases are presented for organic or anorganic aerogels. Within this tiered workflow, aerogels-based materials can be tested in terms of human health hazard.