Several sampling methods were investigated for the quantification of organic anions in the rhizosphere of Al-tolerant (ET8) and Al-sensitive (ES8) wheat plants in soil systems. Controlled environment studies used anion exchange membranes to collect rhizosphere organic anions (from root tips and mature regions of nodal roots) from ET8 and ES8 plants at the 6-leaf stage in a glasshouse environment. Using the anion exchange membranes, a selection of organic anions were detected on the tips and mature regions of roots, with ET8 and ES8 having similar rhizosphere organic anion profiles. The field experiment used 2 established methods of organic anion collection: rhizosphere soil and root washings. The ET8 and ES8 wheat lines had similar levels of organic anions, including malate, in the rhizosphere (using soil shaken from roots and root washings) at 3 sampling times (4 and 6 leaves, and flowering). The rhizosphere organic anions differed significantly from the bulk soil, with the concentration and range of organic anions in the rhizosphere decreasing towards flowering, presumably due to physiological changes in plant and root growth. This study used several techniques to investigate organic anion exudation by roots, with organic anions detected using all techniques. However, technical limitations of these techniques were recognised: (i) the lack of simultaneous exposure of root tips to both the anion exchange membrane and the chemical stimulant, e.g. Al3+; and (ii) the inability to derive the origin of organic anions measured in rhizosphere soil and root washings. The challenge for future soil-based organic anion research is to identify the dominant stress that has triggered an exudation response (i.e. Al toxicity, P deficiency), and to clearly differentiate between plant- and microbial-derived contributions to exudation.