Intracanal medicaments play a vital role in disinfection of root canal system. The aim of this study was to evaluate intratubular penetration and fracture resistance of roots filled with micron- and nano-sized intracanal medicaments: calcium hydroxide (CH), nanocalcium hydroxide (NCH), chitosan (CS) and nanochitosan (NCS). Their antibacterial effect on E. faecalis was tested using agar diffusion method. NCH and NCS were prepared by precipitation method and ionic crosslinking respectively. NCH and NCS particles were spherical, with an average particle size of 102 ± 11.3 nm and 130 ± 17.6 nm respectively. The medicaments were filled in extracted human teeth. Depth of penetration of the medicaments into dentinal tubules at coronal (C), middle (M) and apical (A) thirds was measured. Fracture resistance of the teeth was evaluated after 1 week and 1-month intervals. NCH showed the highest depth of penetration (C ∼746.98 μm, M ∼700.30 μm, A ∼134.69 μm). CS showed the highest fracture resistance, whereas no significant difference was found between other medicaments, at both the time intervals. NCH (8.07 ± 0.06) and NCS (8.13 ± 0.06) showed significantly higher zone of inhibition than CH (7.7 ± 0.17) and CS (7.37 ± 0.15). Under the conditions of this study, it can be concluded that NCH and NCS can be used as potential intracanal medicaments. © 2017 Elsevier B.V.