Most soils are predominantly composed of crystalline minerals which are readily identified by x-ray diffraction, microscopy and spectroscopic techniques. However, reactions between ions in soil solution and soil minerals are commonly dominated by constituents of large specific surface area and high surface chemical reactivity. Such materials frequently occur as nanometric-sized particles in soils and often exhibit a low degree of structural order. Such materials are sometimes referred to by the abbreviation Poorly Ordered Nanoparticulate Materials (PONM)and in many soils the nature and abundance of PONM are poorly understood. In this paper the occurrence of PONM in several Australian soils is described to provide case studies of the nature and origins of the materials and in particular the necessity of using specialised analytical techniques to recognise and characterise such materials. Very poorly ordered alumino silicates with allophanic properties are common minor constituents of humus podzols in many regions of Australia and elsewhere but are rarely recognised in routine soil investigations. However, the allophane often controls the phosphate retention capacity of these soils and this has a major effect on soil fertility and the eutrophication of water bodies receiving drainage from P-fertilised soils. Soils are being drained of acid, saline water in the wheat belt of Western Australia. In this complex geochemical environment diverse PONM form including iron monosulphide, various iron oxyhydroxides including ferrihydrate, akaganeite, goethite and schwertmanite, and aluminium hydroxide. These extremely poorly ordered, nanometric-sized materials are able to sorb diverse heavy metals and other ions, thereby controlling the chemical composition of drainage water from these soils. A third example of PONM in soils relates to the effect of burning (e.g. bush fires) on topsoils which experience full or partial dehydroxylation of alumino silicates and oxyhydroxides to create amorphous or very poorly ordered minerals. Indeed burnt soils are a common feature of several arid to semi-arid regions of the world and there is considerable uncertainty over the abundance and persistence of amorphous, dehydroxylated minerals in such soils. Once again the high chemical reactivity of such materials enables them to exert a disproportional influence on soil chemical behavior. Through these three case studies the application of advanced analytical techniques including selective dissolution procedures, differential XRD and TEM-EDS to the study of PONM is illustrated. The role of synchrotron-XRD and other highly sensitive techniques in the study of PONM will also be discussed by reference to published data.