Background Tuberculosis (TB) is a global public health problem, with the highest burden occurring in low income countries. In these countries the use of more sensitive diagnostics, such as Xpert MTB/RIF (Xpert), is still limited by costs. A cost saving strategy to diagnose other diseases is to pool samples from various individuals and test them with single tests. Positive pool samples are then re-tested individually to identify the patients with the disease. Methods We assessed a pooled testing strategy to optimise the affordability of Xpert for the diagnosis of TB. Adults with presumptive TB attending hospitals or identified by canvassing households in Abuja, Nigeria, were asked to provide sputum for individual and pooled (4 per pool) testing. The agreement of individual and pooled testing and costs were assessed. Results 738 individuals submitted samples, with 115 (16%) being MTB-positive. Valid individual and pooled Xpert results were available for 718 specimens. Of these, pooled testing detected 109 (96%) of 114 individual MTB-positive samples, with 99% overall agreement. Semi-quantitative Xpert Mycobacterium tuberculosis levels had a positive correlation with the smear grades and the individual-positive/pooled-negative results were likely due to the M. tuberculosis concentration being below the detection limit. The strategy saved 31% of cartridge costs. Savings were higher in the community, where the proportion of specimens positive was low. Conclusion The pooled testing strategy had a high level of agreement with individual testing, reduced costs, and has the potential to increase the affordability of Xpert in countries with limited resources.