We estimated the global warming potential of Estonian peatlands (transitional fens and ombrotrophic bogs) based on greenhouse gases (GHG) CO₂, CH₄, and N₂O and carbon (C) accrual in biomass, and the effects of drainage on these processes. Data were derived from a review of the literature of boreal peatlands. Areal estimates of peatland types were multiplied with the values of the interquartile range of literature-derived GHG fluxes. The effect of drainage and radiative forcing of Estonian peatlands were also evaluated. Annual emission of CO₂, CH₄, and N₂O is estimated to be 278 to 1,056 × 10³ of CO₂ equivalent (eq), of which CO₂ makes up 22 to 44%, CH₄ 53 to 73%, and N₂O 3 to 5%. The annual efflux is 419 to 676 × 10³ CO₂ eq year⁻¹ from drained peatlands, and −141 to 380 × 10³ CO₂ eq year⁻¹ from the undrained peatlands. The annual loss of C from peatlands is estimated to be 38 to 86 tons C × 10³ year⁻¹. Thus due to drainage, Estonia's transitional fens and ombrotrophic bogs have gone from being sinks to sources of C.