The aim of this study was to evaluate the effects of sodium hypochlorite (NaOCl), chlorhexidine digluconate (CHX), and mixture of tetracycline, citric acid, and detergent (MTAD) solutions on the surfaces of nickel titanium (NiTi) rotary files with scanning electron microscopy (SEM) and atomic force microscopy (AFM). Irrigation solutions including 2.5% NaOCl, 5% NaOCl, 2% CHX, and MTAD were used. Four new ProTaper rotary NiTi files (F3) were immersed in each four irrigation solutions for 10 min, separately. One untreated NiTi file was used as a control specimen. The surface analysis was performed with SEM and AFM. The surface analysis in AFM was performed on 12 different regions located between first and second millimeters from the tip. SEM images were taken with different magnifications. No surface alteration was recorded under SEM evaluation. AFM revealed that the root mean square (RMS) values of all treated specimens were statistically higher than the control sample (P < 0.05). The sample which was treated with CHX showed lowest RMS values in test groups. All tested solutions caused surface alterations. CHX demonstrated limited surface alterations when compared to the other tested solutions. Microsc. Res. Tech. (c) 2012 Wiley Periodicals, Inc.