A body bias is applied to a non-volatile storage system to compensate for performance variations which are based on the position of a selected word line which is associated with non-volatile storage elements undergoing program, read or verify operations. In one approach, the body bias increases when the selected word line is closer to a drain side of a NAND string than a source side. In another approach, the body bias varies when the selected word line is an end word line. In another approach, first or second body bias levels can be used when the selected word line is in a first or second group of word lines, respectively. The body bias reduces variations in threshold voltage levels and threshold voltage distributions which are based on the selected word line position. Gate-induced drain leakage (GIDL) is also reduced.