Periapical granulomas are sterile or infected have been controversial since long. Various studies mostly used culture methods to evaluate the microbial flora of the periapical lesions, but still landed up with variable and sometimes false positive results. Present study used Modified Brown and Brenn stain to study the presence and location of bacteria in human periapical lesions. Thirty three periapical lesions attached to non-endodontically treated extracted teeth were fixed in 10% buffered formalin, decalcified in 10% HNO3 and were processed for paraffin embedding. Serial sectioning was done and the slides were stained with H&E stain, and Modified Brown and Brenn stain. Of 33 lesions, bacteria were found in 28 lesions (17 granulomas and 11 cysts). Five granulomas were found to be sterile. Majority of the bacteria that were seen were gram-positive cocci, followed by gram-positive bacilli. Gram-negative bacilli were rarely seen. Yeast like structures were also observed in 12 lesions. Knowledge in this field is essential to the clinicians to effectively carryout the endodontic treatment.