The Flies and Eyes project is a community-based, cluster-randomised, intervention trial based in a rural area of The Gambia. It was designed to prove whether flies are mechanical vectors of trachoma; to quantify the relative importance of flies as vectors of trachoma and to test the effectiveness of insecticide spraying and the provision of latrines in trachoma control. A total of 21 clusters, each composed of 300-550 people, are to be recruited in groups of three. One cluster from each group is randomly allocated to receive insecticide spraying, one to receive pit latrines and the remaining to act as a control. The seven groups of clusters are recruited on a step-wise basis separated by two months to aid logistics and allow all seasons to be covered. Standardised, validated trachoma surveys are conducted for people of all ages and both sexes at baseline and six months post intervention. The Muscid fly population is monitored using standard traps and fly-eye contact is measured with catches of flies direct from children's faces. The Flies and Eyes project has been designed to strengthen the evidence base for the 'E' component of the SAFE strategy for trachoma control. The results will assist programme planners and country co-ordinators to make informed decisions on the environmental aspects of trachoma control.