The proportion of patients with recurrent tuberculosis (TB) is reported to be increased in TB patients with human immunodeficiency virus (HIV) infection after they have completed treatment. Despite rising HIV seroprevalence amongst TB patients in Malawi, notifications of patients with relapse smear-positive pulmonary TB (PTB) and recurrent smear-negative TB have remained stable during the past 12 years. We suspected that patients with recurrent or relapse TB were being missed under routine programme conditions. Forty-three hospitals in Malawi were visited in 1999, and TB inpatients who had been registered as 'new' cases in the TB register and treatment card were interviewed about previous episodes of TB. A previous history of TB was elicited in 94 (7.5%) of 1254 patients who were being treated as new cases. Compared with patients with smear-positive PTB, a previous episode of TB was significantly more common in patients with smear-negative PTB (OR 3.5, [95% CI 2.1-5.7], P < 0.001) and patients with extrapulmonary TB (OR 2.0, [95% CI 1.1-3.7], P < 0.05). Of 94 patients with a previous episode of TB, 76 had completed treatment and 18 had defaulted from treatment during this episode. Patients with recurrent or relapse TB are being incorrectly registered within the Malawi TB Control Programme, and in the case of smear-positive PTB patients this is associated with administration of incorrect treatment. Measures have been put in place to rectify the situation, and further operational research is planned to monitor treatment outcomes of patients with recurrent smear-negative TB.