Abstract This study aims to assess methane (CH4) and carbon dioxide (CO2) concentrations in the ventilation systems of two coal mines (A and B) in the Santa Catarina coal deposit in southern Brazil (Paraná Basin, Bonito Formation), and estimate their greenhouse gas (GHG) emissions. The highest CH4 levels (1.8%) were recorded in strong methane emanation areas in mine A, below the lower explosive limit (5%). The IPCC-recommended methods significantly overestimated the methane emission (up to 80%) when compared to the experimental data measured for each mine. Application of an alternative method made it possible to estimate direct CO2 emissions, indicating that CO2 accounted for 22 to 77% of total GHG emissions. Carbon dioxide emissions are generally not included in GHG emission inventories, indicating that the coal industry underestimates the contribution of this gas. As such, it is recommended that the methodology used for these calculations be revised and that specific emission factors be applied for each mine. In order to improve the accuracy of inventories, more sampling needs to be carried out in all operational and abandoned mines.