We have used high-resolution neutron Larmor diffraction and capacitative dilatometry to investigate spontaneous and forced magnetostriction in undoped, antiferromagnetic YBa$_2$Cu$_3$O$_{6.0}$, the parent compound of a prominent family of high-temperature superconductors. Upon cooling below the Neel temperature, $T_N = 420$~K, Larmor diffraction reveals the formation of magneto-structural domains of characteristic size $sim 240$~nm. In the antiferromagnetic state, dilatometry reveals a minute ($4 times 10^{-6}$) orthorhombic distortion of the crystal lattice in external magnetic fields. We attribute these observations to exchange striction and spin-orbit coupling induced magnetostriction, respectively, and show that they have an important influence on the thermal and charge transport properties of undoped and lightly doped cuprates.