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 usually needs increasing proportions of 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 (with□being the symbol for a vacant site). Less commonly, the short-range configuration Ca(Al2□)Al6(BO3)3[Si5T3+O18]V(OH)3W(OH) could occur in Al-rich tourmalines with a Si deficiency, where T3+= B, Al. Therefore, tourmalines enriched in cations with charge 2 + (Fe2+, Mn2+, Mg) contain only insignificant Y-site vacancies. Aluminum-rich tourmalines with ≥ 7.0 apfu Altotalthat 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. If no chemical data for Li is available it is proposed to calculate the Li content in such colourless or coloured tourmalines (elbaite, fluor-elbaite, fluor-liddicoatite, rossmanite) 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 from the schorl-dravite series with MgO > 1.0 wt% (and only minor amounts of Fe3+, Cr3+and V3+) 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.