This study evaluated a relatively new molecular technique, serial analysis of gene expression (SAGE), as a tool for quantifying gene expression in the ovine abomasal nematode Haemonchus contortus for which there is relatively limited (~20% gene coverage) sequence information. SAGE technology generates data that are both qualitative and quantitative and, as such, compliments other functional genomics approaches such as EST analysis and micro-array. Prior to embarking on large-scale comparisons, the present study was initiated to establish (i) how well SAGE and EST data taken from the same life-cycle stage would compare, (ii) how easily SAGE tags could be assigned to genes given that the genome sequence is not available and (iii) whether it would be possible to extend the sequences of the SAGE tags to facilitate their identification. Of 2825 tag sequences analysed from adults harvested 28 days post-infection, the identity of the encoding gene could be ascribed to 63% of the tags. The relative abundance of these genes, arbitrarily categorized on the basis of function, was comparable with that of an EST dataset also from adults (n=2317). In addition, tag sequences could be readily extended and thereby identified using a tag-based primer and Reverse Transcription-PCR.