Are you comparing cells  in the same row  (e.g.) A1 with B1 or in a different
row?

If A1 and B1 are different which one do you want to colour?

Could you do this better by using conditional formatting rather than a macro?

I am comparing the cells  between different rows.
Lets say A and C. A is default and C needs to be
colored if its different.

So, Set a conditional format

in, say, C1
Format/Conditional Format
Condition: not equal to A1 (make sure you use A1 not $A$1)
Format: borders and shading, Fill, Red
Then copy this down from C1 however far you want to go. You can use the
format painter to do this if the cells  have already been filled.