The effects of pesticides on the general population, largely as a result of dietary exposure, are unclear. Adopting an organic diet appears to be an obvious solution for reducing dietary pesticide exposure and this is supported by biomonitoring studies in children. However, results of research into the effects of organic diets on pesticide exposure are difficult to interpret in light of the many complexities. Therefore future studies must be carefully designed. While biomonitoring can account for differences in overall exposure it cannot necessarily attribute the source. Due diligence must be given to appropriate selection of participants, target pesticides and analytical methods to ensure that the data generated will be both scientifically rigorous and clinically useful, while minimising the costs and difficulties associated with biomonitoring studies. Study design must also consider confounders such as the unpredictable nature of chemicals and inter- and intra-individual differences in exposure and other factors that might influence susceptibility to disease. Currently the most useful measures are non-specific urinary metabolites that measure a range of organophosphate and synthetic pyrethroid insecticides. These pesticides are in common use, frequently detected in population studies and may provide a broader overview of the impact of an organic diet on pesticide exposure than pesticide-specific metabolites. More population based studies are needed for comparative purposes and improvements in analytical methods are required before many other compounds can be considered for assessment.