This study compared dentinal and apical crack formation after instrumentation with different nickel-titanium systems at two different working lengths (WL) in large and small canals. Two hundred and eighty human teeth were randomly distributed into two control and 12 experimental groups (n=20 each). Large and small canals were instrumented by the WaveOne, Protaper Universal System (PTU), Twisted File (TF), or Twisted File Adaptive (TFA) at 1 mm shorter than canal length (CL-1 mm) or 1 mm beyond apical foreman (CL+1 mm). Horizontal sections were microscopically observed to evaluate the dentinal cracks (only large canals). Scanning electron microscopy images were taken before and after instrumentation to assess apical cracks. All file types caused more apical cracks in small canals than in large canals regardless of the WL. During over-instrumentation (WL=CL+1 mm), the WaveOne and PTU groups developed significantly more dentinal cracks at the 6 and 9 mm sections than the TF and TFA groups.