SETTING: Most countries endemic and highly endemic for tuberculosis (TB) still do not have reliable TB surveillance systems. Indirect estimation of TB incidence is needed to monitor the performance of the National Tuberculosis Programme (NTP) in the context of the World Health Organization implementation and impact targets for TB control. OBJECTIVE: To estimate the case detection rate (CDR) of all TB cases and sputum smear-positive TB cases in Egypt in 2007. METHODS: Record linkage and three-source capture-recapture analysis of data collected through active prospective longitudinal surveillance within the public and private non-NTP sector in four Egyptian governorates selected by stratified cluster random sampling. RESULTS: For all TB cases, the estimated CDR of NTP surveillance and completeness of case ascertainment after record linkage was respectively 55% (95%CI 46-68) and 62% (95%CI 52-77). For sputum smear-positive TB cases, these proportions were respectively 66% (95%CI 55-75) and 72% (95%CI 60-82). CONCLUSION: This pilot study shows that representative sampling, prospective surveillance in the non-NTP sector, record linkage and capture-recapture analysis can improve CDR estimation. For global, standardised and reliable use, this methodology should be further developed. Until then, all resource-limited countries should strengthen their national surveillance systems in the context of the Stop TB strategy.