Ciliary alignment is considered necessary to establish respiratory tract 4 mucociliary clearance, and disorientation is o en associated with primary 5 ciliary dyskinesia. erefore, there is an urgent need for a detailed analy-6 sis of ciliary orientation (CO). We used volume electron microscopy to ex-7 amine CO relative to the tracheal long axis (TLA) by measuring the inter-8 and intracellular basal body orientation (BBO) and axonemal orientation 9 (AO), which are considered to coincide, both equivalently indicating the 10 e ective stroke direction. Our results, however, reveal that only the mean 11 BBO is aligned with the TLA, whereas the AO determines the e ective 12 stroke direction as well as the mucociliary transport direction. Further-13 more, we show that even if the mean CO is conserved across cell bound-14 aries, a considerable gradient in CO exists within individual cells, which 15 we suspect to be crucial for the emergence of coordinated ciliary activity. 16 1 Our ndings provide new quantitative insight into CO and correlate this 17 new structural information with mucociliary function. 18 Introduction 19 e epithelium of the tracheobronchial tree constitutes a self-cleaning surface, which mainly 20 consists of secretory goblet cells and ciliated cells. Dust and infectious particles enter the 21 respiratory tract when breathing. Due to adhesion, these particles get entrapped by the mucus 22 layer lining the inner surface of the airways. Coordinated movements of billions of subjacent 23 cilia then propel the overlying mucous carpet towards the larynx, thereby cleaning the lungs 24 from inhaled substances. 25 Cilia are hair-like protrusions of the cell membrane with a particular cytoskeletal sca old 26 called axoneme. e ciliary axoneme consists of an evolutionary preserved 9+2 microtubular 27 structure: a central pair is surrounded by nine circularly aligned microtubule doublets. e 28 microtubules arise from the basal bodies, which are anchored to the cytoskeleton and serve as 29 nucleation sites for the growth of axonemal microtubules. e chiral structure of the axoneme 30 as well as of the basal foot appendage allows to unequivocally determine ciliary orientation 31 (CO). 32 e physical orientational alignment of motile cilia along the proximal-distal axis of the 33 airways is a prerequisite for concerted directional ciliary movement and the generation of 34 directed uid ow (e.g. Vladar et al. (2015); Guirao and Joanny (2007)). Studies a empting to 35 quantify the orientation of respiratory cilia usually determined the direction of the assumed 36 ciliary beating plane, or more speci cally, the direction of the 'e ective stroke' (or 'power 37 stroke'). According to the literature, the e ective stroke direction is unambiguously de ned, 38 and can be inferred from two chiral ciliary structures: 1) the ciliary beating plane is assumed 39 to be perpendicular to the central pair of microtubules, and in particular, the e ective stroke 40 is assumed to be directed from doublet 1 towards the gap between doublet 5...