We present a novel technique for creating template-free probabilistic maps of the cytoarchitectonic areas using a groupwise registration. We use the technique to transform 10 human post-mortem structural MR data sets, together with their corresponding cytoarchitectonic information, to a common space. We have targeted the cytoarchitectonically defined subregions of the primary auditory cortex. Thanks to the template-free groupwise registration, the created maps are not macroanatomically biased towards a specific geometry/topology. The advantage of the group-wise versus pairwise registration in avoiding such anatomical bias is better revealed in studies with small number of subjects and a high degree of variability among the individuals such as the post-mortem data. A leave-one-out cross-validation method was used to compare the sensitivity, specificity and positive predictive value of the proposed and published maps. We observe a significant improvement in localization of cytoarchitectonically defined subregions in primary auditory cortex using the proposed maps. The proposed maps can be tailored to any subject space by registering the subject image to the average of the groupwise-registered post-mortem images.