Herein we report the study of the influence of synthesis conditions during the microwave-hydrothermal crystallization of freshly precipitated gels on the phase composition and morphology of the rare-earth doped yttrium orthophosphates nanoparticles. We characterize the nanoparticles of YPO sub(4) and YPO sub(4) times 0.8H sub(2)O using X-ray diffraction analysis, TEM, and FT-IR spectroscopy. Furthermore, we argue that for the given phase the degree of crystallinity and thus the sample morphology depend strongly on the synthesis conditions. We establish that the hexagonal hydrate phase can be obtained by means of microwave-hydrothermal method if one uses phosphate anion excess or adjusts pH of the reaction mixture. Also we show that the metastable hydrate phase is most likely stabilized by hydroxyl groups at elevated temperatures.