Purpose The purpose of the study was to compare three recent Life Cycle Impact Assessment (LCIA) models in prioritizing substances and products from national emission inventories. The focus was on ecotoxic and human toxic impacts. The aim was to test model output against expert judgment on chemical risk assessment. Materials and methods An emission inventory was collected for Finland describing the year 2005. The inventory included publicly reported emissions to air and water and it was complemented by the emissions of tributyltin, benzene, and pesticides from research papers and statistics. The emissions were characterized with three LCIA models: IMPACT 2002+, ReCiPe, and USEtox and priority substances were identified. The results were connected to an environmentally extended input-output model to study priority products and supply chains. A comparison was made with two integrated assessments of the chemical status and human exposure in the Baltic region. Results and discussion The three assessed models presented very different priorities. In ecotoxicity, IM-PACT2002+ and USEtox highlighted heavy metals while ReCiPe focused on tributyltin. The integrated assessment identified both groups. In human toxicity, IMPACT2002+ and the integrated assessment focused on organic air pollutants while USEtox and ReCiPe identified mainly metals.Conclusions LCIA models can be used for priority setting in chemical emission control and consumption based analyses. However the models give differing prioritizations so care must be taken in model selection. The studied models differed from expert assessment mostly in substances which are bioaccumulative. Further studies in including bioaccumulation to LCIA models of toxic impact are recommended.