Objectives: This systematic review aims to discuss the shaping properties and outcomes of nickel-titanium (NiTi) rotary and reciprocation systems assessed by micro-computed tomography. Data source: A literature search was conducted in PubMed and SCOPUS database until April 2018 to identify investigations examining the shaping properties and outcomes of rotary and reciprocation NiTi systems using micro-computed tomography. In addition, a quality assessment was undertaken for the included studies. Results: A total of 1,110 titles were identified in the literature search. After removal of duplicates, 25 studies satisfied the inclusion criteria. Quality assessment showed that 17 studies were of low risk of bias. Six shaping properties and outcomes including centering ability, transportation, untouched canal walls, canal surface area and volume, microcrack formation, and debris accumulation were discussed. Conclusions: The use of the same system in rotary or reciprocation motions and reciprocating single file systems have comparable transportation and centering ability. No difference was observed between rotary and reciprocation systems/motions in surface area and volume of the canal changes. Untouched canal walls and accumulation of debris remained controversial. No relationship was found between kinematics of instrumentation and the formation of dentinal cracks. Keywords: micro-computed tomography, nickel-titanium, reciprocation, rotary, shaping properties