Symmetry breaking of the left-right body axis is a crucial step in development for many vertebrate species. In many this is initiated with a directional cilia-driven fluid flow in the organising structure. This work focuses on the mouse and the zebrafish organising structures, the node and Kupffer's vesicle, wherein cilia perform a tilted rotation producing an asymmetric flow. Using singularities of Stokes flow, slender body theory and the boundary integral equation, a computational model of flow in the mouse node for a range of cilia configurations simulating developmental stages is developed and run on the University of Birmingham's cluster, BlueBEAR. The results show the emergence of a directional flow as the cilia tilt increases. To model the Kupffer's vesicle the regularised boundary integral equation is used with a mesh representation of the entire domain to investigate potential cilia mechanisms that produce the observed flow as there is not a consensus. The results show that a combination of the experimental observations could be a sufficient mechanism. This model is expanded using observations of cilia with two rotation frequencies which are incorporated by allowing such cilia to ‘wobble’. This wobble accentuates the asymmetric flow in wildtype embryos and diminishes it in mutant embryos. All of these results agree well with experiment suggesting that vertebrates develop a combination of rotation mechanisms in their organising structures before an appropriate symmetry breaking flow is established.