Application of organic residues to soil is generally assumed to improve soil tilth. Only few studies have reported on the long-term effects on the more subtle aspects of soil porosity and no reports have considered the potential effects of organic amendments on the pore system in the subsoil. We sampled undisturbed soil cores (100 cm3 and 6280 cm3) in metal cylinders in differently fertilized plots in the long-term field experiments at Askov Experimental Station, Denmark. We selected the 0-60 cm soil layer of plots dressed for a century with either mineral fertilizers (labelled NPK) or animal manure (labelled AM). Both fertilization treatments were studied at two levels of nutrient application: 'normal' (labelled '1') and 1.5 times 'normal' (labelled '11/2'). Plots unfertilized for a century (labelled UNF) were included as a reference for some of the studies. Water retention, air permeability and air diffusivity were measured on the small cores, and we used the large cores for measuring near-saturated and saturated hydraulic conductivity. In the plough layer, the AM and NPK soils displayed identical pore volumes in size fractions larger as well as smaller than 30 micrometer, while the UNF soil had a significantly smaller volume of pores <30 micrometer. No clear trends were found in treatment effects on pore organization calculated from air diffusivity and air permeability measurements. No significant differences in hydraulic conductivity were found for plough layer soil. For the soil below ploughing depth, significantly larger macropore volumes and near-saturated hydraulic conductivities were found for soil receiving the higher ('11/2') amount of nutrients compared with the 'normally' dressed soil. This effect was independent of fertilization system (AM or NPK). We attribute the larger volume of macropores to the improved root growth conditions in the soil with the larger nutrient level. We conclude that addition of animal manure in rates realistic in agriculture has only a modest effect on soil pore characteristics of the plough layer soil compared with the use of mineral fertilizers. For the soil below ploughing depth, a high level of nutrient application rather than the use of animal manure may increase soil macroporosity and near-saturated hydraulic conductivity.