Jatropha curcas seed oil is a promising feedstock for biodiesel production. The seeds contain major toxic (phorbol esters, PEs) and antinutritional (phytate and trypsin inhibitor) factors. In the present study the localisation of antinutrients and a rapid qualitative method for detecting the presence of PEs were investigated.Kernels were separated into cotyledon, hypocotyl, kernel coat and endosperm. The majority of phytate (96.5%), trypsin inhibitor (95.3%) and PEs (85.7%) were localised in the endosperm. Based on PEs, a qualitative method was developed to differentiate between toxic and non-toxic Jatropha genotypes. In this method, PEs were easily detected by passing methanol extracts of kernels (Jatropha toxic and non-toxic genotypes) through a solid phase extraction (SPE) column and measuring the absorption of the resulting eluates at 280 nm. For raw kernels, SPE eluates with absorbance ≥ 0.056 were considered as toxic and those with absorbance ≤0.032 as non-toxic. For defatted kernel meals, SPE eluates with absorbance ≥ 0.059 were considered as toxic and those with absorbance ≤0.043 as non-toxic.The majority of antinutrients/toxic compounds are localised in the endosperm of the kernel. The qualitative method developed for rapid identification of toxic PEs could be useful in screening the toxicity of Jatropha-based products in the biodiesel industry. Further confirmation of PEs should be established by high-performance liquid chromatography.