Background Chlamydia control in England is based on management of positives and their partners (partner notification) and on identifying asymptomatic infections in the community (screening).

Aims To describe the relative contribution of screening and partner notification to control of chlamydia at different stages in the epidemic and evaluate optimal resource allocation to each control.

Methods Using pair approximation equations we investigate the efficacy of control programmes for chlamydia on short time scales that are relevant to policy makers. We estimate prevalence, incidence, and positivity in those screened and in their partners. We combine these measures with a costing tool to estimate the economic impact of different public health strategies.

Results Increasing screening coverage significantly increases the annual programme costs whereas an increase in tracing efficiency initially increases annual costs but over time reduces costs below baseline, with tracing accounting for around 10% of intervention costs. We found that partner positivity is insensitive to changes in population prevalence due to screening, remaining at around 33%.

Conclusions Maintaining efficacy of partner notification is cost-effective at all stages of the epidemic (stable/declining prevalence) but becomes increasingly cost-effective as control measures reduce the population prevalence.