Raman spectroscopy has been employed in analytical sciences for purity determination of carbon nanotube samples based on the consideration of G-/D-band intensity ratios. This work demonstrates the role of aggregation in these feature bands, which, in the case of single walled carbon nanotubes (SWNTs), has proved to be crucial for G-/D-band intensity ratio measurements. We have found variation in the relative intensities of G- and D-bands across a sample of SWNTs without any other treatment, discarding the possible influence of the laser beam or sample focusing. In the case of multiwalled carbon nanotubes (MWNTs), this effect is less notorious. Thus, to achieve a good representativeness of Raman measurements, it is important to consider the sample preparation procedure in order to avoid aggregation, which has an effect over the signals, making difficult the subsequent interpretation of results.