The associations between histopathology and imaging remain elusive and investigating underlying reasons of tumor microstructure resulting in an imaging phenotype is of clinical importance. The present study used cross-sectional guided biopsy specimen to employ the exact spatial biopsy localization to correlate the prebioptic magnetic resonance imaging (MRI) with immunohistochemical stainings of the histopathological specimen. Twenty-seven patients with mass-forming cholangiocarcinoma (CCA) were included in the present analysis. All patients were imaged by a 1.5 T clinical scanner at last one month before the biopsy. The contrast enhanced dynamic sequences were analyzed with quantified signal intensities. The bioptic specimen were obtained by cross-sectional guided biopsy and was further analyzed with cell density, proliferation index (Ki67), tumor-infiltrating lymphocytes, tumor-stroma ratio as well as Collagen. There were no statistically significant correlations between the signal intensities of the MRI with cell count, tumor-stroma ratio, Ki67 index and CD45 count. Only a moderate correlation was identified between relative signal intensities of the venous phase with the Collagen-stained area (r=0.40, p=0.04). DCE MRI is not associated with histopathology features in CCA. The complex interactions of the tumor and the tumor micromilieu are not reflected by the MRI phenotype.