There is controversy over if interstitial cystitis considered an autoimmune disease, or could it be part of a lupus flare? lupus causes inflamation.

Not likely: There is a layer, the GAG layer in the bladder that protects against some of the chemicals in the urine which are irritating/inflammatory if they come in contact with the lower layers. In interstitial cystitis, that layer is absent. The questions revolve around what causes the loss of that layer. I have not seen any studies implicating lupus. Lupus can cause inflamation in any organ, however.

IC and Lupus: IC (Interstitial Cystitis) is inflammation of the Bladder Wall that can occur by itself or in conjunction with other autoimmune diseases, including Lupus, fibromyalgia, scleroderma, and Sjogren's Syndrome. Research has shown that IC patients are 30 Times more likely to have SLE (systemic lupus erthematosus). If you have IC, tests for Autoimmune conditions should be performed by your Doctor.