Interstitial Cystitis (IC) is a common urinary tract condition affecting up to 1 in 10 U.S. women. IC is hallmarked by urinary urgency, frequency, and abdominal pain with bladder filling. Currently, many aspects of IC are poorly understood. Diagnosis of IC is inconsistent and often inaccurate. Many substances and cells are passed in the urine that may serve as markers for identifying patients with IC. Currently there are no widely used urinary or genetic markers for IC. Studying gene expression in shed urinary epithelial cells may help identify patients with IC. Developing a more accurate evaluation tool may help avoid misdiagnosis and delay in treatment. We hypothesized that cells shed in the urine of IC sufferers exhibit a differential gene expression pattern compared to non-affected controls. Our study was a pilot project that enrolled 23 subjects to compare cells sloughed in the urine samples of control vs. IC subjects. DNA microarray was used to compare gene expression. To our knowledge, there have been no other similar studies conducted. Three significant findings arose from our project. The first is that RNA is extractable and quantifiable from cells sloughed in the urine. The second is that RNA is stable in TRI reagent across a wide variety of temperatures. The third finding is that differential gene expression is found in IC subjects compared to controls. The findings of this study encourage further investigation on a larger scale to confirm these preliminary findings.