This article provides a comparative analysis of the regulation of ammonia emissions, primarily from livestock installations, in Denmark, Germany and the Netherlands. It discusses the challenges of regulating agricultural ammonia emissions in view of the rulings of the Court of Justice of the European Union (cjeu) on Art. 6(3) of the Habitats Directive. It is argued that the need to ensure certainty concerning the absence of significant effects on Natura 2000 sites is challenged by the uncertainties regarding both the state of individual habitat types and the potential impact of individual projects. A more integrated or programmatic approach may provide an alternative approach to individual assessments, but it is necessary to ensure that additional loads from new or enlarged livestock installations are permitted in areas with high ammonia loads only where it is certain that a programmatic approach will ensure that there are no harmful effects. This might be an almost impossible task.