The reduction of warpage of organic substrates is one of the challenges in flip chip package applications, since the warpage affects the manufacturability of chip joining and potentially, the solder joint reliability. Mechanical simulation of organic substrates results in a warpage shape that reflects the symmetry of the circuitry pattern, often in a bowl shape, when the circuitry pattern is taken into account. However, the actual substrates manufactured often exhibit warpage shapes that are randomly distorted and are different from each other even when they have identical circuitry design patterns and are segmented from the same panel. Potential causes for the spread in warpage shapes are inhomogeneities in processes or environmental conditions during manufacturing which can lead to an in-plane variation or fluctuation in substrate properties. In this report, the deformation of organic substrates under in-plane variations of substrate properties are analyzed by mechanical simulation. A simple substrate structure with a plane copper and an insulating dielectric layer on both sides of the core layer was used as the model for the analysis. Potential varying properties are material properties such as elastic modulus and coefficient of thermal expansion. The form factors such as layer thicknesses can also vary along the in-plane direction. In our analyses, the in-plane variations as a whole are incorporated in simulation as a change in cure shrinkage rate of insulating dielectric layers in order to generate various warpage shapes. The cure shrinkage rate was used, since it is temperature independent in simulations by finite element method (FEM). Linear variations with lateral length scales of the substrate size are applied. Several configurations of variations are studied by changing the positions of maximums of the cure shrinkage rate. The analyses revealed that the configuration of variations is an important factor in determining the warpage shape of a substrate. The analysis also showed that the balance of property between front layers and back layers of the substrate has a great influence in determining the warpage shapes. The analysis of the in-plane layer thickness variation showed that the magnitude of warpage for insulating dielectric layer is greater than that for the conductive layer. The result suggests that the control of the uniformity of properties and thickness of insulating dielectric layers are important in reducing the warpage caused by inhomogeneity of properties occurring during manufacturing processes. The warpage analysis of the in-plane property variation was also conducted for a test substrate with a 3-2-3 build-up layer structure to examine the effects of in-plane property variation on warpage of patterned substrates. The results showed that the warpage of a substrate with a symmetric circuitry pattern results in an asymmetric shape when an asymmetric in-plane property variation occurs. The warpage caused by circuitry pattern overlaps with that caused by in-plane property variation. It suggests that the reduction of warpage is possible for the substrates with properties of known trends in inhomogeneity by applying an appropriate compensation in the circuitry design.