We found that two BBS genes (BBS5 and BBS7) are required for axonal outgrowth, whereas one transition zone gene (NPHP1), four BBS genes (BBS9, BBS10, BBS11 [TRIM32] and BBS12) and an IFT regulator, KIF7, modulate neurite outgrowth and filopodial formation, indicating the differential and specific influence of ciliopathy genes over post-migratory neuronal differentiation. Here, BBS2 is linked to ciliopathy.