A new methodology based on maximum likelihood estimation for structure refinement using powder diffraction data is proposed. The method can not only optimize the parameters adjusted in Rietveld refinement but also parameters to specify errors in a model for statistical properties of the observed intensity. The results of structure refinements with relation to fluorapatite Ca5(PO4)3F, anglesite PbSO4, and barite BaSO4 are demonstrated. The structure parameters of fluorapatite and barite optimized by the new method are closer to single-crystal data than those optimized by the Rietveld method, while the structure parameters of anglesite, whose values optimized by the Rietveld method are already in good agreement with the single-crystal data, are almost unchanged by the application of the new method.