Despite the fact that there exists several techniques capable of characterizing the nanoparticle sizes, their measurement results from the same sample often deviate from each other at an amount that is considered significant in the nanometer scale. The principles of measurements these techniques or instruments based upon might contribute a notable portion to the disagreement of the measurement results. The sample preparation itself could only further add to the complexity of the problem. In the absence of international standards, or world-wide recognized protocols dealing with nanoparticle characterization, a comparison study was carried out to investigate the systematic deviations in measuring nanoparticle diameters. Three types of commonly used nanoparticle sizing instruments, Photon Correlation Spectroscopy (PCS), Atomic Force Microscopy (AFM), and Transmission Electron Microscopy (TEM) were utilized to take measurements on traceable polystyrene latex samples at 100 nm, 50 nm, and 20 nm in diameter. The final analysis showed a fairly satisfactory agreement of the measured data from the samples' certified values, with the exception of the result from the Field-Emission TEM (FE-TEM). It was later determined that the major source of the deviation was attributed to the instrument rather than to the sample. Instrument calibration was the course of action taken to bring the outlier to the desired accuracy. Additionally, discussions were also made with regards to the need of standardization in nanoparticle measurements.