The coordinated movement of pit-cell cilia in the ventral node creates fluid flow that facilitates left-right asymmetry during mouse development. To achieve this, pit cells are polarised along the anteroposterior axis by the planar cell polarity (PCP) pathway that positions the basal body at the posterior end of the cell. Although the mechanism behind basal body positioning has been unclear, Hiroshi Hamada and colleagues now reveal the role of basal body-associated microtubules (baMTs). The authors show that the PCP proteins Dchs1 and Dchs2 do not exhibit anteroposterior polarity themselves, but they are required for the anterior localisation of the PCP pathway protein Vangl1. By using small molecules that affect cytoskeleton dynamics, the authors reveal that microtubules and actomyosin networks are required for the positioning and maintenance of the basal body in cultured tissue. Finally, careful in vivo image analyses show that baMTs become asymmetrically organised in a PCP-dependent manner: anterior or posterior baMTs extend horizontally or vertically, respectively. baMT organisation occurs after anterior localisation of Vangl1 but before basal body positioning. Together, these data show that asymmetric baMT organisation may position the basal body in pit cells for symmetry breaking.