We sought to assess the feasibility and reproducibility of performing tissue-based immune characterization of the tumor microenvironment using CT-compatible needle biopsy material. Three independent biopsies were obtained intraoperatively from one metastatic epithelial ovarian cancer lesion of seven consecutive patients undergoing surgical cytoreduction using a 16-gauge core biopsy needle. Core specimens were snap-frozen and subjected to immunohistochemistry (IHC) against human CD3, CD4, CD8 and FoxP3. A portion of the cores was used to isolate RNA for (1) real-time quantitative (q)PCR for CD3, CD4, CD8, FoxP3, IL-10 and TGFβ, (2) multiplexed PCR-based T-cell receptor (TCR) CDR3 V-β region spectratyping and (3) gene expression profiling. Pearson's correlations were examined for immunohistochemistry and PCR gene expression, as well as for gene expression array data obtained from different tumor biopsies. Needle biopsy yielded sufficient tissue for all assays in all patients. IHC was highly reproducible and informative. Significant correlations were seen between the frequency of CD3+, CD8+ and FoxP3+ T cells by IHC with CD3-epsilon, CD8A and FoxP3 gene expression, respectively, by qPCR (r = 0.61, 0.86 and 0.89; all p < 0.05). CDR3 spectratyping was feasible and highly reproducible in each tumor, and indicated a restricted repertoire for specific TCR V-β chains in tumor-infiltrating T cells. Microarray gene expression revealed strong correlation between different biopsies collected from the same tumor. Our results demonstrate a feasible and reproducible method of immune monitoring using CTcompatible needle biopsies from tumor tissue, thereby paving the way for sophisticated translational studies during tumor biological therapy. © 2011 Landes Bioscience.