Background: Galactokinase catalyses the first committed step of galactose catabolism in which the sugar is phosphorylated at the expense of MgATP. Recent structural studies suggest that the enzyme makes several contacts with galactose - five side chain and two main chain hydrogen bonds. Furthermore, it has been suggested that inhibition of galactokinase may help sufferers of the genetic disease classical galactosemia which is caused by defects in another enzyme of the pathway galactose-1-phosphate uridyl transferase. Galactokinases from different sources have a range of substrate specificities and a diversity of kinetic mechanisms. Therefore only studies on the human enzyme are likely to be of value in the design of therapeutically useful inhibitors. Results: Using recombinant human galactokinase expressed in and purified from E. coli we have investigated the sugar specificity of the enzyme and the kinetic consequences of mutating residues in the sugar-binding site in order to improve our understanding of substrate recognition by this enzyme. D-galactose and 2-deoxy-D-galactose are substrates for the enzyme, but N-acetyl-D-galactosamine, L-arabinose, D-fucose and D-glucose are all not phosphorylated. Mutation of glutamate-43 (which forms a hydrogen bond to the hydroxyl group attached to carbon 6 of galactose) to alanine results in only minor changes in the kinetic parameters of the enzyme. Mutation of this residue to glycine causes a ten-fold drop in the turnover number. In contrast, mutation of histidine 44 to either alanine or isoleucine results in insoluble protein following expression in E. coli. Alteration of the residue that makes hydrogen bonds to the hydroxyl attached to carbons 3 and 4 (aspartate 46) results in an enzyme that although soluble is essentially inactive. Conclusions: The enzyme is tolerant to small changes at position 2 of the sugar ring, but not at positions 4 and 6. The results from site directed mutagenesis could not have been predicted from the crystal structure alone and needed to be determined experimentally.