BACKGROUND Advances in root canal instruments have led to lesser frequency of dentinal crack formation. Not many studies have been reported in literature that compare crack formation using instruments based on control memory (CM) and M wire technology. The study intended to evaluate and compare the prevalence of dentinal cracks formed by ProTaper Next (Dentsply Maillefer, Ballaigues, Switzerland), HyFlex CM (Coltene, Whaldent) and Wave One (Dentsply, Maillefer) reciprocating file systems at the apical and middle third of the mesiobuccal root canal of mandibular molars under scanning electron microscope (SEM). METHODS Forty-five extracted sound human mandibular molars were decoronated and mesial roots were retained followed by root canal instrumentation using ProTaper Next, HyFlex CM and WaveOne reciprocating files. Roots were then sectioned perpendicular to the long axis of teeth and viewed under scanning electron microscope to detect the presence of cracks. RESULTS ProTaper Next system produced more cracks compared with HyFlex and Wave One (P < 0.05) but there was no statistically significant difference between all the three groups. All the file systems showed more incidences of cracks in the apical third compared to middle third. CONCLUSIONS All the NiTi instruments produced cracks and the highest incidence of cracks was seen in the apical third compared to middle third region. KEY WORDS Dentinal Cracks, HyFlex CM, ProTaper Next, Root Canal, Wave One