The use of anti-chlamydial antibiotics for trachoma control is based on the assumption that most people with clinically active disease have conjunctival infection with Chlamydia trachomatis. In high prevalence areas, this is generally true. As prevalence decreases, however, the positive predictive value of clinical signs for C. trachomatis infection also decrease. In this paper, the case for using laboratory assays to guide trachoma control strategies is presented, molecular methods for diagnosis (such as a ligase chain reaction and a polymerase chain reaction [PCR]) are compared with earlier techniques, and recent findings of ongoing studies using a quantitative PCR are reviewed. In addition, the contribution of genotyping to our understanding of the epidemiology and biology of C. trachomatis is considered.