BackgroundDespite great efforts to control Tuberculosis (TB), progress is compromised by low adherence to medication, leading to prolonged duration of infectiousness and continued transmission. Investigating low adherence is of high importance from TB programmatic perspective. Though data on actual days of missed treatment exist, the effect of such on TB cure rates has not been investigated.MethodsTB operational research data were extracted for smear-positive pulmonary TB patients registered at Zomba Central hospital, Malawi from January 2007 to December 2008.ResultsOf the 524 patients, 302 (57.6%) were males and 340 (64.9%) fully adhered to treatment. Excluding 5 individuals with missing data on cure, four hundred and eighty-one (92.7%) were cured of TB, and of these 162 (33.7%) missed at least one day of treatment. Respectively, 49/64 (76.6%) and 71/76 (93.4%) of those who missed treatment in the intensive and continuation phases were cured of TB (p = 0.005). The adjusted logistic regression analysis showed that those who missed 15–29 days of treatment (OR = 0.04, 95% CI: 0.01, 0.14) were less likely to be cured of TB compared with those who fully adhered.ConclusionTreatment non-adherence was high and was observed even within the first 2 months of treatment. Thus, even at an earlier critical stage of treatment, simple algorithms need to be developed to identify and monitor patients at higher risk of non-adherence. Efforts on treatment compliance counselling should focus on enhanced counselling to improve adherence during the intensive treatment phase.