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I can not find a study that compares the 2 chemos. The biggest difference seems to be cost. Gemcitabine costing $37 vs Mitomycin C $1068 per instillaation
“In summary, intravesical installation with gemcitabine reduces the recurrence rate in patients with low grade disease by almost 50%. The installation is safe, well tolerated and cost-effective compared to the current standard (mitomycin-c). Gemcitabine should become the standard installation agent for those suspected with low or intermediate risk non-muscle invasive bladder cancer.”