Disclosed herein are compositions and methods for reducing expression of C90RF72 mRNA and protein in an animal with C90RF72 specific inhibitors. Also disclosed herein are compositions and methods of selectively inhibiting a C90RF72 pathogenic associated mRNA variant by administering an antisense compound targeting the region beginning at the start site of exon 1A to the start site of exon 1B of a C90RF72 pre-mRNA. Such methods are useful to treat, prevent, or ameliorate neurodegenerative diseases in an individual in need thereof. Such C90RF72 specific inhibitors include antisense compounds.