Due　to　the　effect　of　gravity　on　machine　tools,　the　small　deformations　inevitably　exist.　The　existing　tolerance　allocation　methods　are　based　on　the　rigid　body　assumption,　which　ignore　the　small　deformations.　It　will　make　optimization　results　inaccurate　and　increase　manufacturing　cost.　Therefore,　a　new　optimal　tolerance　allocation　method,　which　integrates　the　small　deformations,　is　presented　in　this　paper.　The　establishment　of　a　geometric　error　model　based　on　tolerance　is　involved　at　first.　Based　on　this　model　and　multi-body　system　theory,　the　mapping　relationship　between　tolerance　and　volumetric　error　of　the　five-axis　machine　tool　(FAMT)　is　formulated.　Secondly,　the　small　deformations　of　the　FAMT　are　obtained　based　on　finite　element　analysis.　Then,　the　optimal　tolerance　allocation　model　is　established　by　integrating　the　small　deformations　into　the　constraint　conditions.　Thirdly,　simulation　analysis　is　carried　out　with　this　model　by　using　a　genetic　algorithm.　Then,　the　optimal　tolerance　allocation　scheme　is　obtained,　and　the　total　manufacturing　cost　after　optimization　is　reduced　by　approximately　11.5%.　Finally,　the　volumetric　errors　of　the　FAMT　are　calculated　based　on　the　two　tolerance　allocation　schemes.　The　results　show　that　the　volumetric　errors　are　within　the　permitted　ranges.　Therefore,　the　proposed　method　in　consideration　of　the　small　deformation　is　feasible　and　effective.