Since introduction of alternative fuels and it’s integrations in the cement industry in the past four decades, it has received more attentions by raising the energy costs in the last decade. Using alternative fuels such as; solid waste and tire may decrease the energy costs that affects on cement cost price. Despite using solid wastes as alternative fuels in the cement industry of some countries affects, there is no significant work in Iran. Although one can find many industrial of academic results on this subject, there are still some doubts (about using alternative fuels) such as: effects of using alternative fuels on the productive clinker quality, clinker conditions, exiting gases, budgets for permanently using alternative fuels and old tires are proposed as the wealth back period. In this project, most primitive alternative fuels in the cement industry. A brief description on injection systems, alternative fuels, its advantages, disadvantages and previous works in this area are presented. Then by using the genetics algorithm, software a code for optimizing the amounts of alternative fuels and raw materials in this system is presented. This algorithm is able to give optimum amounts of raw materials and alternative fuels, in the cost function, while it satisfies the constrains and also clinker properties. The results show, that even a 100% replacement of fuels by waste tires without negative effects on the clinker is possible. In the second part of the written software, by determining the chemical analysis of the raw materials fuels, the new clinker conditions including cooking temperature, production, phases, air volume, exiting gas volume are specified. The result that reveals there are insensible changes in the system, except some changes in the volume of existing gases due to using tire fuels. In the next step, An economical assessment for using 10% alternative fuel (tire) in the line 2 of Bojnourd Cement Company was performed. The results show that using alternative fuels in the Bojnourd cement industry and probably in other cement factories is economical and do not increase current expenditures. In the last section A preliminary design for the channel of injecting tires to clinker, and the installation position is proposed. Keywords : alternative fuels, cement industry, clinker, optimization