Metastasis accounts for nearly 90% of all cancer associated mortalities. A hallmark of metastasis in malignancies of epithelial origin such as in the pancreas and breast, is invasion of the basement membrane (BM). While various in vitro assays have been developed to address questions regarding the invasiveness of tumors with relation to the BM, most fail to recapitulate a physiologically accurate cell-membrane interface. Here, we introduce a new 3D in vitro assay that uses the mouse mesenteric tissue as a mimic for the epithelial BM. We describe a simple, cost-effective protocol for extraction and setup of the assay, and show that the mesentery is a physiologically accurate model of the BM in its key components—type IV collagen, laminin-1 and perlecan. Furthermore, we introduce a user-friendly quantification tool, Q-Pi, which allows the 3D reconstruction, visualization and quantification of invasion at a cellular level. Overall, we demonstrate that this invasion assay provides a physiologically accurate tool to investigate BM invasion.