OBJECTIVES: To quantify default during diagnosis in TB suspects and in smear-positive cases; to investigate sex differences in default during diagnosis, in all of Pakistan. METHODS: Data from laboratory registers were collected on 12 216 suspects in nine districts over the period July-September 2008. RESULTS: A total of 1573 TB suspects (12.9%, 95% CI = 12.3-13.5) dropped out of the diagnostic process after initial sputum submission. A total of 2058 smear-positive cases were detected, and of these 107 (5.2%, 95% CI = 4.2-6.2) defaulted during diagnosis and therefore could not be started on treatment. Male suspects defaulted slightly more frequently than female suspects (P = 0.0268). CONCLUSION: Default during diagnosis is a frequent occurrence in Pakistan that should be monitored and addressed by TB control programs.