Successful root canal therapy requires an accurate diagnosis and management of complex root canal morphology. Although the occurrence of three root canals in maxillary and mandibular premolars is very rare, the clinician must be able to identify it clinically and radiographically to make the necessary changes in his shaping and obturation techniques. We present the endodontic management of a maxillary first premolar with three separate roots and canals, which was diagnosed with the aberrant anatomy only after the access preparation. Then, a mandibular premolar with three root canals and fused roots, which were diagnosed radiographically, is presented. The necessary modifications of the routine clinical steps and the application of dental operating microscope for successful management of the complex anatomy, with emphasis on access modifications and radiographic interpretations are also explained. Teeth with extra roots and/or canals pose a challenge in clinical management. Identifying them early is necessary to facilitate appropriate modifications in treatment protocol, armamentarium to be used and plan optimal number of treatment sittings.