Measuring farmland biodiversity is time-consuming and costly.  Operational data from the Farm Scale Evaluation of genetically modified crops project were collated to identify the financial and time costs of each of the 14 protocols used.  A subset of 113 of the 266 experimental sites was used.  The mean overall cost per site was £19 453 (£ of 2002).  Laboratory time was almost 2.5 times that in the field.  The most costly protocol was soil surface invertebrates because it required species level identification.  The 'bees and butterflies' protocol at £418 per site was particularly cost-effective.  The six vegetation protocols accounted for 65% and the six arthropod protocols accounted for 29% of the total costs.  The recommended reduction from 12 to 3 transects would have saved £1356 per site, 6% of total budget.  A minimalist approach using the single-season seedbank protocol would cost £3437 per site.  The effect of geographical spread of sites on cost was small because of clustering of sites and the large number of protocols.  Careful selection of ecological indicators can save considerable resources.