Tourmaline has two different [6]-coordinated sites, the Y site and the Z site. Vacancies were reported from both sites. Based on high-quality chemical and single-crystal structural data it always needs increasing proportions or short-range order configurations Na(Al2⊏)Al6(BO3)3[Si6O18]V(OH)3W(OH) or Na(Al2⊏)Al6(BO3)3[Si6O18]V(OH)3WF in order to produce Y-site vacancies. Therefore, tourmalines enriched in cations with charge 2+ (Fe2+, Mn2+, Mg) contain only insignificant Y-site vacancies. Only Al-rich tourmalines with >7.0 apfu Altotal that usually contain >0.2 apfu Li may have significant vacancies at the Y site. However, no more than 12% vacancies (0.36 pfu) at the Y site can be observed in such samples. It is proposed to calculate the Li content in such colourless or coloured tourmalines (elbaite, fluor-elbaite, fluor-liddicoatite, rossmanite), if no chemical data for Li is available, for Y = 2.8 apfu or for Y + Z + T = 14.8 apfu, because this calculation should give more accurate results than calculating the Li content as the difference to 3.0 apfu at the Y site. For Fe2+-rich and Mg-bearing tourmalines (schorl-dravite series) with MgO >1.0 wt% the structural formula can still be calculated for Y + Z + T = 15 apfu, because such tourmalines do not appear to contain significant Y-site vacancies. It can further be concluded that the Z site could be only <1% vacant and therefore such vacancies would be insignificant even in Al-rich tourmaline.