Aim: To compare the canal transportation using three different rotary and reciprocating single file systems. Subjects and methods: Sixty mesiobuccal roots of human permanent maxillary molars free of caries, cracks and restoration were taken. Pre and post instrumentation CBCT scans of all the roots were taken. Instrumentation was performed with the help of Hyflex EDM, Neolix Neoniti and S-One endodontic files. All the roots were examined at 3, 5 and 7mm from the radiographic apex. Results: At the coronal 7mm from the apex there was no significant difference between the files. At the middle 5mm S-One performed better than both the rotary file system, while at the apical 3mm all three file systems showed significant results as S-one performed better than Hyflex EDM followed by Neolix Neoniti. Conclusion: S-One single reciprocating file preserved better canal anatomy than both the other rotary file systems.