Although rotary NiTi endodontic instruments have widespread use, there is need for improved clinical performance. Objective: Utilize Micro-X-ray Diffraction (Micro-XRD) and SEM to investigate phase relationships and surface topography for two brands of instruments modified by a new Plasma-Immersion Ion Implantation (PIII) technique. Methods: ProFile 0.04 taper and ProTaper F2 rotary instruments (Dentsply/Maillefer) were selected. For PIII preparation (AISI 316, APT, Germany), samples were chosen randomly from as-received instruments. Nitrogen ion, or nitrogen plus argon ion, implantation was performed at 25 kV target voltage and incident dose of 5x1017 ions/cm2. Micro-XRD (Rint-2000, Rigaku) was performed with CuKα radiation at 40 kV and 300 mA tube voltage and current, respectively. Analyses of 50 µm diameter areas were obtained at the tip of each instrument and 3, 6, 9 and 12 mm from the tip. The sample stage was oscillated to minimize the effect of preferred orientation. Each instrument was examined with an SEM before and after surface modification. Results: Micro-XRD detected TiO2 and tentatively Ni3N on the surfaces of as-received ProFile instruments, but not ProTaper instruments, nor any instruments after PIII processing. The strong austenite 110 peak and weaker 211 peak were observed for both instruments; peaks were generally weakest in the tip region. The 200 austenite peak was very weak for ProFile instruments and not observed for ProTaper instruments. Preferred orientation of austenite existed in both instruments. Some martensite peaks may be obscured by the broad 110 austenite peak. SEM observations were consistent with Micro-XRD analyses. Deposits were observed on the surfaces of electropolished as-received ProFile instruments. No additional surface changes were evident from PIII processing. Conclusions: Because PIII is carried out near room temperature, there is no significant alteration of bulk NiTi phases. The effect of in vitro instrumentation on PIII-modified surfaces requires further study, which is in progress.