The aim of this work was to check whether commercially available enzymes are pure enough to be used for selenium speciation analysis and the contribution that impurities could make to Se determination in real samples. For this purpose, twelve commercially available enzymes with different origins and classifications (protease, amylase, cellulase, lipase) were analysed. After the dissolution of the enzyme in water, the Se species were separated by ion exchange chromatography, with inductively coupled plasma mass spectrometry used as the detection system. The results showed that the Se content was significant in several cases. The highest value was obtained for beta-amylase from barley, 3100 ng Se per g of enzyme. Speciation analysis showed that Se-methionine, selenite, selenate and some unknown compounds were present in several enzymes. In general, the Se species identified represented a small fraction of the total Se. For instance, only 17% of the total Se was determined for beta-amylase from barley. On the other hand, about 100% of the total Se was identified in protease from Streptomyces griseus. Upon comparing the results from different lots of the same enzyme, not all of them were found to be comparable. Thus, the presence of selenium species in commercially available enzymes could be due to the preparation procedure used for the enzyme; they could be present as degradation products. Therefore, when determining selenium species in samples with low Se contents, attention should be paid to enzyme purity in relation to selenium compounds when an enzyme is used for hydrolysis.