The purpose of this paper is to introduce the gas exchange measurement and flux calculation methods commonly used in the projects of the programme "Greenhouse gas emissions from the use of peat and peatlands in Finland". The methods include measurements of instantaneous fluxes of CO2, CH4 and N2O made at the ecosystem-atmosphere boundary using closed chamber, and whole ecosystem fluxes of the gases using micrometeorological EC tower extending above the canopy, and the integration of seasonal and annual fluxes. In addition, tools developed for gap filling of missing weather records, and generating complete weather patterns for the key environmental controls of the gas fluxes are introduced. Derivation of emission factors from the collected gas fluxes, capable of reproducing the dynamic, climate dependent nature is outlined.