In-cylinder flow study is important to understand the fuel mixing , combustion and emissions in diesel engines. The initial flow pattern is set up by the intake stroke as free vortex and is subsequently modified during compression stroke as forced vortex. This paper deals with in-cylinder flow comparison for two different geometries of the intake manifold (Standard and Screw Threaded) of a single cylinder direct injection diesel engine. The scope of using screw threads is to improve the swirl motion of the intake air. Modified geometry involves an internal screw threaded intake manifold (forming a protrusion into the manifold) with defined pitch, cross-section and length of the helix path. An experimental study using a steady state flow rig(Paddle Wheel Type) has been performed on the standard geometry to obtain mass flow coefficient and swirl ratio. Steady state CFD simulations are performed on both the geometries using ANSYS FLUENT as solver and compared with the experimental data. Effect on mass flow coefficient due to resistance from screw threads to the intake air has been studied. To understand the effect of compression stroke on swirl parameters, a transient simulation is run for both geometries to capture the flow during intake and compression stroke. Swirl flow inside the cylinder is characterized by swirl ratio. Swirl ratio varies with crank angle and is compared for both the geometries. Various flow parameters like turbulent kinetic energy, velocity streamlines and velocity components on a section plane were also studied.