An LCA study on the production of an Italian brand of high quality milk (bottled in 1 l Tetra Top®) was carried out in compliance with the Product Category Rules for milk of the International EPD® System. The results were compared with the registered environmental product declaration (EPD) of another brand of milk. The most relevant source of differences between the two studies is the choice of different system models, mainly due to lack of detailed instructions in PCR, especially for: fertilizers field emissions and choice of the models for their estimation; inclusion of the complementary fodder production; waste management. The results of this analysis were used to participate in the open consultation of the PCR revised version and to highlight the importance of including more detailed instructions. After the publication of the updated version of the PCR, the LCA study was revised for the part of the inventory concerning methane emissions from cattle and emissions due to manure management and spreading. The impact assessment results show that raw milk production at farms is the most critical life cycle phase, mainly because of: CH4 from enteric fermentation, CO2 from diesel consumption, and N2O and NH3 airborne emissions as well as NO3− waterborne emissions coming from manure management and fertilizers use. Therefore, reductions of the environmental impacts can be mainly obtained at farms, with, for example, the selection of a diet for reducing enteric emissions, the introduction of energy recovery from anaerobic digestion of manure, the optimisation of the use of fertilizers adopting precision farming techniques. The results are within the literature range of values, though not fully comparable because of the existing differences in assumptions and modelling choices. Recommendations for improving the comparability of LCA in the food sectors are outlined.