Primary cilia are cellular appendages important for signal transduction and sensing the environment. Bardet-Biedl syndrome proteins form a complex that is important for several cytoskeleton-related processes such as ciliogenesis, cell migration and division. However, the mechanism by which BBS proteins may regulate the cytoskeleton remain unclear. We discovered that Bbs4 and Bbs6 deficient renal medullary cells display a characteristic behaviour comprising poor migration, adhesion and division with an inability to form lamellipodial and filopodial extensions. Moreover, few cells were ciliated (48% ± 6 for WT cells vs 23% ± 7 for Bbs4 null cells) and bear shorter cilia (2.55 μm ± 0.41 for WT cells vs 2.16 μm ± 0.23 for Bbs4 null cells). Whilst the microtubular cytoskeleton and cortical actin was intact, the actin cytoskeleton was severely disrupted, forming abnormal apical stress fiber aggregates. Furthermore, we observed over-abundant focal adhesions in Bbs4, Bbs6 and Bbs8-deficient cells. In view of these findings and the role of RhoA in regulation of actin filament polymerisation, we showed that RhoA-GTP (activated form) levels were highly upregulated in the absence of Bbs proteins. Upon treatment of Bbs4-deficient cells with a RhoA inhibitor, Y27632, we were able to restore cilia length and number as well as the integrity of the actin cytoskeleton. Together these findings indicate that Bbs proteins play a central role in the regulation of the actin cytoskeleton and control cilia length through alteration of RhoA levels.