In this paper, present-day emissions of greenhouse gases and acidifying compounds from agriculture are analysed at the farm level. Quantitative estimates are given for these emissions from three nested systems in the Netherlands: the agricultural sector, greenhouse horticulture, and tomato cultivation under glass. Total emissions are subdivided into emissions from biogenic sources and abiogenic sources. We conclude that, although most of the emissions from the agricultural sector have biogenic sources, those from abiogenic sources should not be neglected. Abiogenic emissions are mainly from greenhouse horticulture. The cost-effectiveness of options to reduce carbon dioxide (CO2) and nitrogen oxides (NOx) emissions from on-farm combustion of natural gas in tomato cultivation under glass is analysed. An inventory is given of technical reduction options that are presently available in practice. Based on information about the costs and the reduction potential of each option, cost-efficiency curves are derived for both types of emissions. Relative to a situation where none of the described options were applied (early nineties), CO2 and NOx emissions from tomato cultivation can be reduced at most by about 70 nd 75°respectively, by combinations of technical options.