In recent years there has been growing interest in replacing (genetically modified) soya by lupin. Lupin seeds, flours and lupin containing food have been analyzed in order to assess the relevance of a potential health hazard given by mycotoxins and/or naturally occurring alkaloids. Since not all important alkaloids used for quantitation were commercially available, isolation of lupanine, 13alpha-hydroxylupanine and angustifoline from lupin flours of high alkaloid contents was performed. Alkaloids were analyzed by GC-MS/GC-FID in parallel, while the phomopsin mycotoxins were analyzed by ELISA, since chromatographic methods were not sensitive enough and required time-consuming sample cleanup. The analyzed lupin containing foods were free of phomopsins. In foods where lupin was only a minor constituent the alkaloid content was of no concern. However, roasted lupin beans intended as coffee surrogate had alkaloid contents close to the Australian intervention limit of 200 microg/g.