Urine is often acidic when it is first excreted. Thus urine will etch the marble. It will take more than cleaning to return the appearance to a pre-urine condition.
Standard cleaning procedure with SX-15 and Stone Perfect or your favorite spinner tool and alkaline cleaner works most of the time when followed by polishing. If the marble was not sealed or the stain is more extensive, you may need to pretreat with a mild acid like TCU Neutralizer. The good news is that since the urine already etched the marble, any etching from your mild acid pretreatment gets polished out when you are polishing the original etch mark. Spinergy pads can quickly feather the affected are into the same gloss level as the surrounding marble.