Ammonia emissions from both traditional and new welfare-based housing systems for laying hens must be reduced to prevent detrimental effects on the environment. In a comparative study, the effect of manure handling (variation in drying and removal frequency) in a battery cage and the effect of manure handling (as in battery cage system) and litter treatment (removal of litter) in a Tiered Wire Floor (TWF) aviary system on the emission of ammonia were investigated. Each system housed 6480 hens, treatments were varied in time, and effects were analysed by means of time-series analysis. The hens in the TWF system dropped 22.5% of their excreta in the litter and the remaining part, like all manure in the battery cage system, was dropped on the manure belts. The estimated emission from the manure on the belts in both systems was 18.8 g/h (daily mean, manure removal twice a day), whereas the emission from the litter in the TWF system amounted to 62.5 g/h. Emission from the belt manure on a typical day increased by 14, 39, 109 and 177% from the 1st until the 4th day after manure removal. The effect of increasing temperature and water vapour pressure difference on emission was 17% and -22% per degree and per kPa, respectively. Drying of manure on the belts increased the dry matter content of the manure and showed a tendency towards lower emissions. The dry matter content of the litter varied between 780 and 840 g/kg, the mean total nitrogen content was 3.3% of the dry matter, and the layer thickness varied between 2 and 9 cm. Both the ammonia content, which ranged between 20 and 190 mg/kg, and the layer thickness of the litter influenced the emission from the litter positively.