Several conditions. True holes in the iris can be created surgically, caused by trauma, or arise from certain congenital or genetic defects. Often, there can be the appearance of a hole caused either by an area of thick iris surrounding a region with less pigment (this really is a "valley" called a crypt), or a dark freckle (nevus) on a lighter iris.
Need more info. I am not sure what "holes" you refer to. If you have in mind black "dots" occasionally seen in one's iris, those are benign lesions that just don't have a normal pigment accumulation. If you do have symptoms or those "holes" are just bothersome in appearance, it won't hurt to consult optometrist or ophthalmologist for an in-depth exam.