The response of five inbred sunflower seedling lines, including AC 4122, C, HA 89, HA 410, HA 411, to inoculation with Sclerotinia sclerotiorum culture filtrate containing endogenous oxalic acid was compared with the exogenous application of synthetic oxalic acid. The reaction of seedlings was evaluated in terms of dry and fresh plant weights and the total chlorophyll concentration relative to untreated controls. The expression of shikimate dehydrogenase in cotyledons was also assessed five days after treatment. The results indicated that exogenous oxalic acid inoculation caused more deleterious effects on stem rot, eliciting photosynthesis reduction and different isoenzyme patterns of shikimate dehydrogenase. A positive correlation was found between increased oxalic acid and shikimate dehydrogenase activity in both treatments. However, the excessive toxicity of the exogenously administrated acid suggests that Sclerotinia sclerotiorum infection triggers a more complex metabolic pathway involving oxalic acid secreted by the pathogen. These observations preclude the possibility of using the synthetic acid administration as a method of screening sunflower genotypes for resistance to Sclerotinia. In addition to these findings, the reactivation of shikimate dehydrogenase was observed in both treatments. In contrast to synthetic administration, expression during the first phase of growth may serve as a tool for rapid screening and selection of sunflower genotypes resistant to Sclerotinia sclerotiorum.