A least squares refinement with a generalized structure factor expression in the Gram-Charlier expansion was applied to the structure of elbaite, XY₃Z₆(BO₃)₃T₆O₁₈A₃⁽¹⁾A⁽²⁾ (X = Na_0.640Ca_0.090K_0.006[]_0.264, Y = Al_0.415Fe²⁺_0.084Mn²⁺_0.034Mg_0.005Ti⁴⁺_0.003Li_0.458, Z = Al, T = Si, A⁽¹⁾ = (OH)_0.750, and A⁽²⁾ = F_0.179(O,OH)_0.071). Elbaite has space group R3m, and hexagonal cell dimensions of a = 15.874(3) and c = 7.116(3) Å. The least squares refinement of the X-ray single-crystal data measured at room temperature converged at R = 0.0221 for 179 variables, including terms up to the fourth order coefficients. The O1 and O2 sites showed multiple split probability density functions (pdfs), and the X site showed a circular ring-like pdf, providing evidence of positional disorder at these sites. The disorder at the O1 and O2 sites was interpreted to be due to substitutional disorder of the Y site cations. The remaining atom sites all showed unimodal pdfs with a more or less asymmetric tendency along the hexagonal c-axis. The asymmetry is related to the primary effect of pyroelectricity.