No tool exists to identify potential under-diagnosis of smear-negative and extrapulmonary TB. In an ecological study, we used a simple tool plotting percentages of smear-positive pulmonary TB amongst newly diagnosed TB in African region countries and provinces in Mozambique against the country’s and provinces’ HIV prevalence. We visually inspected the plots to determine potential under-diagnosis of smear-negative and extrapulmonary TB in three facilities in Manica Province, Mozambique. In these facilities, we found 67% smear-positivity among new TB cases in an area with HIV prevalence of more than 10%. All African region countries with an HIV prevalence of more than 10% had a smear-positivity lower than 50%. Most Mozambican provinces with a high HIV prevalence have smear-positivity rate of below 51%. Our findings show that benchmarking can be used to assist in identifying potential under-diagnosis of smear-negative and extrapulmonary TB. The findings also suggest that potentially under-diagnosis of these forms of TB exists in the study population. © Brouwer et al.; Licensee Bentham Open.