Abstract Small structural changes in bulk metallic glasses (BMGs) following thermal treatment below the glass-transition temperature were observed. Zr-based BMG ingots with nominal compositions of Zr 52.5Cu 17.9Ni 14.6Al 10.0Ti 5.0 (at.%) were isothermally annealed at 630 K for 10–60 min in vacuum and then cooled down. Structural relaxation was indicated by enthalpy evolution during differential scanning calorimetry and by changes in micro-hardness. Atomic structure was studied using time-of-flight neutron diffraction followed by a pair-distribution function (PDF) analysis. Observed changes in the PDF could not be explained by a “free volume” annealing, but were consistent with the elimination of short and long inter-atomic distances.