Interstitial Cystitis (IC) is a chronic and painful bladder syndrome of unknown cause with no reliable biologic marker or effective therapy. Vascular endothelial growth factor (VEGF), which plays a key role in bladder inflammation, is closely associated with the vascular alterations observed in patients with IC. However, our recent findings of VEGF receptors and co-receptors on non-endothelial cells in human and mouse urothelium suggest that additional VEGF targets and functions are possible in IC bladders. We report here that VEGF receptors and co-receptors (neuropilins, NRP) are strongly expressed in both the human bladder urothelium and in the human bladder cancer cell line (J82), and that the expression of NRP2 and VEGF-R1 are significantly down-regulated in IC when compared to control subjects. In addition, treatment of J82 cells with Bacillus Calmette-Guérin (BCG), a novel treatment strategy for IC, up-regulates the messages for NRPs and VEGF-Rs. Furthermore, intravesical instillation of an internalizable VEGF fluorescent tracer (scVEGF/Cy5.5) into mouse urinary bladders results in a marked ligand accumulation in the urothelium and bladder parenchyma indicating that urothelial VEGF-Rs are functionally active, and capable of ligand interaction and internalization. Our results suggest that the VEGF pathway is altered in IC, that urinary VEGF may gain access to the bladder wall via these receptors, and that BCG treatment may replenish the missing VEGF/NRP receptors. Together these results suggest that levels of NRPs, VEGF-Rs, and VEGF are new putative markers for the diagnosis of IC and that modulating these receptors can be exploited as therapeutic strategies.