The aim was to evaluate apical debris extrusion produced by a single-file system used in counter-clockwise reciprocation and compare it to rotary single-file systems used in clockwise rotation and clockwise reciprocation. A total of 100 first mandibular molars were divided into five groups (n = 20): (i) WaveOne Gold Glider and Primary instrument in counter-clockwise reciprocation; (ii) One G and One Curve file in clockwise rotation; (iii) One G and One Curve file in clockwise reciprocation; (iv) TruNatomy Glider and Prime instrument in clockwise rotation; and (v) TruNatomy Glider and Prime instrument in clockwise reciprocation. Apical debris extruded was measured after glide path preparation and canal preparation. WaveOne Gold displayed significantly higher amounts of apical debris extrusion in all the groups (P < 0.05). The lowest mean values were recorded by clockwise reciprocation groups: TruNatomy Glider, One Curve and TruNatomy Glider and Prime combined value, for glide path, canal preparation and combined mean values, respectively.