Synthesis of TiO2 anatase nanocrystals by hydrothermal methods often results in the formation of small quantities of brookite, which is difficult to eliminate by tuning the reaction conditions and is usually present in the final nanomaterial. The effect of this impurity on the Raman spectrum in anatase nanomaterials has not been fully explored. In this work, a study on the effect of reaction temperature on the position and line shape of the low-wavenumber Raman peak is presented. A comparison of the spectra of nanomaterials of pure anatase and anatase with brookite impurity (4–13 nm), synthesized by hydrothermal microwave heating, is made. It is shown that the low-wavenumber Raman peak (100–300 cm–1) for pure anatase nanocrystals is strongly dependent on the nanocrystal size and that the peak position is well described by the phonon confinement model (PCM). For anatase nanocrystals with 15% brookite impurity, the spectrum shows an asymmetric band, which is formed mainly by the contributions of the anatase Eg and brookite A1g modes, with the brookite B1g and B3g peaks further broadening the band. In addition, the PCM no longer describes the peak position. These results show that even a small amount of brookite can have a strong influence on the Raman spectra of anatase/brookite-impurity samples.