Background: Microorganisms in the root canal system are considered to play a major role in the pathogenesis of apical periodontitis. The present study was conducted to compared ethylenediaminetetraacetic acid, maleic acid, and peracetic acid in smear layer removal from instrumented root canal system. Materials & Methods: 40 non-carious human anterior teeth with single root were divided in groups. Group I was maleic acid group: 07%, group II was PAA group: 0.5%, group III was the EDTA group: 17% and group IV was the control group: 0.9% saline. These teeth were then evaluated using SEM analysis for the absence or presence of smear layer. Results: At coronal third, score 1 in group I was seen in 100%, 15% in group II, 100% in group III and 12% in group IV. Score 2 was seen in 85% in group II and 88% in group IV. Score 3 was not seen in any groups. At middle third, score 1 in group I was seen in 75%, 50% in group II, 65% in group III and 0% in group IV. Score 2 was seen in 25% in group I, 35% in group II, 35% in group III and 30% in group IV. Score 3 was seen in 15% in group II and 70% in group IV. At apical third, score 1 in group I was seen in 62%, 0% in group II, 60% in group III and 12% in group IV. Score 2 was seen in 38% in group I, 62% in group II, 25% in group III and 0% in group IV. Score 3 was seen in 38% in group II and 15% in group III and 100% in group IV. The difference was significant (P< 0.05). Conclusion: 7% maleic acid as a final irrigant is highly efficacious for the removal of smear layer when used in the apical third of the root canal system.