Infection with Mycobacterium tuberculosis is a major cause of death worldwide. Identification of mycobacteria in tissue sections is usually easily achieved by acid-fast stains, but this method sometimes gives unsatisfactory results. The authors therefore compared conventional staining techniques and polymerase chain reaction (PCR) for mycobacterial DNA sequences in 24 selected tissue samples from patients with tuberculosis. In all samples, either positive or negative with acid-fast stain, mycobacterial DNA fragments were detected. In addition, tissue samples from patients with clinically proven sarcoidosis were included as controls. Surprisingly, strong signals for mycobacterial DNA were found in 2 of 15 cases. Polymerase chain reaction is a useful technique in the demonstration of mycobacterial DNA fragments in patients with clinically suspected tuberculosis who have acid fast stain-negative histology. An epithelioid granulomatous reaction in the lung, negative by acid-fast stain and positive for mycobacterial DNA by PCR, however, does not permit a diagnosis of tuberculosis, because a positive result can also be obtained in cases of sarcoidosis. In some cases of sarcoidosis, the causal agent might be either cell wall defective mycobacteria or persistent intracellular DNA from mycobacteria.