Diesel engine can be run with biodiesel which has the potential to supplement the receding supply of crude oil. As biodiesel possess similar physiochemical properties to diesel, most diesel engines can run with biodiesel with minimum modifications. However, the viscosity of biodiesel is higher, and the calorific value is lower than diesel. Therefore, when biodiesel is used in diesel engines, it is usually blended with diesel at different proportions. Use of 100% biodiesel in diesel engines shows inferior performance of having lower power and torque. Improving in-cylinder airflow characteristic to break down higher viscous biodiesel and to improve air-fuel mixing are the aims of this research. Therefore, guide vanes in the intake runner were used in this research to improve the performance of diesel engine run with biodiesel. Previous research done by the authors using CFD cold flow simulations (no combustion) showed an improvement of air-biodiesel mixing with guide vanes installed into the intake runner in a diesel engine. In this research, vane height was varied experimentally to find the effect of vane height on the performance of a CI engine run with biodiesel. Subsequently, five guide vanes models with varied vane height were fabricated and tested. The other parameters of the vanes such as angle, length and number were kept constant at 35°, three times the radius of the intake runner and four. The results of brake specific fuel consumptions, engine efficiency and engine torque of the CI engine run with all five guide vane models of varied vane height were then compared with the one having no guide vanes. Generally, a reduction of BSFC and increment of engine efficiency were observed when the CI engine was run with guide vanes as compared to the one without guide vanes while the torques were remained same for both cases.