Manganese‐doped yttrium aluminum perovskite (YAP) nanocrystalline samples of 0.05 at%, 0.2 at% and the reference single crystal of predicted 0.02 at% Mn, 0.02% Si concentration in YAP were investigated by the following methods: X‐ray powder diffraction, scanning electron microscopy, EPR, SQUID and XPS. These examinations revealed that the obtained material was not single phase and the trace of Y3Al5O12 (YAG) appeared. As is evident from EPR studies, the manganese in all investigated samples is occupying an yttrium site and the valence of manganese remains as Mn2+. The EPR spectra of both powder YAP:Mn samples are the same, an expected difference in the intensity well reflects the nominal concentration of manganese. The single crystal perovskite YAlO3 doped with manganese showed very complex and strongly anisotropic EPR spectrum. The EPR data showed the presence of Mn2+ ions substituting yttrium site and Cr3+ and Fe3+ undesirable impurities which occupied aluminum site. The magnetic moments of manganese calculated for the nanopowders confirmed Mn2+ state. The SEM/EDS and XPS analyses showed the chemical composition of nanopowders as very consistent for both methods. For both samples the lower content of aluminum in relation to the nominal value was found. The SEM images show that the sample 0.2 at% Mn has more agglomerated structure. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)