The butterfly effect is a phenomenon seen in some roots and is related to density of dentinal tubules. The aim was to investigate penetration depth and adaptation quality of root canal sealers and ProRoot MTA into bucco-lingual and mesio-distal aspects of roots with and without the effect. One hundred and twenty teeth were decoronated at the cemento-enamel junction. Canals were prepared and assigned to obturation groups: gutta-percha with a sealer (AH Plus, EndoREZ, Kerr Pulp Canal Sealer, MTA Fillapex) or ProRoot MTA alone (each containing 10 butterfly and 10 non-butterfly roots). Root sectioning yielded coronal and middle samples. Confocal laser scanning and scanning electron microscopy were used to assess penetration and adaptation. Teeth with the effect had greater mean penetration bucco-lingually (766 μm) than mesio-distally (184 μm, P = 0.003). Coronal sections had greater penetration (430 μm) compared with middle (247 μm, P = 0.006). In conclusion, greater penetration in roots with the effect may improve treatment outcomes.