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Nanocrystalline biocompatible single-phase Mn-doped A-type carbonated hydroxyapatite (A-cHAp) powder has been synthesized by mechanical alloying of a stoichiometric mixture of CaCO3, CaHPO4·2H2O and MnO powder for 10 h at room temperature under open air. The A-type carbonation in HAp (substitution of CO3(2-) for OH(-)) is confirmed by FTIR analysis. Microstructure characterization in terms of lattice imperfections and phase quantification of ball milled samples are made by analyzing XRD patterns employing the Rietveld structure refinement method. Rietveld analysis of XRD patterns recorded from Mn-doped HAp samples has been used to locate Mn(2+) cations in HAp. The Ca2 vacancy site is found to be more favorable for Mn substitution. Microstructure characterization by HRTEM corroborates the findings of the X-ray analysis where the presence of a significant amount of amorphous phase of HAp analogous to indigenous bone mineral is clearly found. MTT assay shows sufficiently high percentage cell viability confirming the cytocompatibility of the sample.