The contribution deals with the problem of safety assurance in machinery in accordance with the requirements of the Directive 2006/42/EC of the European parliament and of the Council of 17 May 2006 on machinery, and amending Directive 95/16/EC (recast), replacing the Directive 98/37/ES. The existing methods suitable for identification of hazards associated with machinery are reviewed. A new method of risk assessment in machine tools is presented, applying the system approach to hazard identification and to analysis and evaluation of risks associated with machinery, in accordance with the relevant Czech and EU legislation. Further, the contribution discusses a suitable way of documenting the risk assessment process.