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The aim of this study was to determine relationships between ammonia and hydrogen sulphide emissions and the type of manure storage, and correlations between emissions and Estonian climatic conditions. Total ammonia (NH3) and hydrogen sulphide (H2S) emissions depend directly on the open area of manure storage. Of ring-shaped manure storage, with permanent roofing (H1, open area 3.9 m2), 2.7 kg NH3 and 0.02 kg H2S were emitted per year. Emissions from plastic lagoons (H4, open area 4100 m2) were 920 kg NH3 and 4.6 kg H2S per year. Emissions per animal unit (AU) per year from storage H1 were 14.6 g NH3 and 0.08 g H2S, and from storage H4 722.8 g NH3 and 3.65 g H2S. The emission of pollutants, per m2 of open area also depended on the depth of stored manure. The highest emissions were from the ring-shaped uncovered storage systems with high walls (H2), at 1.05 g m-2 24h-1. Emissions from ring-shaped uncovered storage with low walls (H3) was 25% smaller, 0.79 g m-2 24h-1, and from the manure lagoons (H4) 42% lower, 0.61 g m-2 24h-1. However the variation between storage systems was not significant (P > 0.05). Temperature (°C) had the greatest effect on increasing ammonia emission (r = 0.65***). The correlation between temperature and hydrogen sulphide emissions was not significant (r = 0.18). Relative humidity (%) had no effect to ammonia and hydrogen sulphide emission (r = 0.02 and 0.16 respectively).