The aim of this study was to evaluate the influence of using waste materials, such as tires or meat meal, as a secondary fuel during clinker production on the polychlorinated dibenzo-p-dioxin (PCDD)/polychlorinated dibenzofuran (PCDF) emission levels to the atmosphere. For this purpose, three different cement plants in Spain were chosen to conduct the project in different sampling episodes. Different materials were separately evaluated in each plant: the first plant included the addition of meat meal in the kiln, the second plant used rejected tires, and the third plant used a mixture of both. In all cases, PCDD/F emission values remained below the limit established by the European Union Directive of 0.1 ng I-TEQ/Nm3, with values ranging from 0.001 to 0.042 ng I-TEQ/Nm3. The major contribution to total TEQ in the majority of cases came from 2,3,7,8-tetrachlorodibenzofuran owing to its relatively higher levels and 2,3,4,7,8-pentachlorodibenzofuran because of its TEF of 0.5. The remaining 15 toxic congeners collectively provided only a minor contribution to TEQ. Furthermore, no marked differences were found compared with reported data obtained from Spanish cement kiln plants using conventional fuel. This fact indicates that the addition of used tires or meat meals had no effect on PCDD/PCDF emission levels.