An inverse analysis of the flow of capsules in a square section microfluidic channel has been proposed to evaluate the elastic modulus of the membrane of microcapsules. It is based on the comparison of the capsule deformed profiles measured experimentally with the ones computed numerically in the same flow situation. Experimentally, the microchannel is never exactly square. The objective of this paper is to evaluate the intrinsic error, which is made by analyzing the flow of a capsule in a slightly rectangular channel by means of the numerical results obtained in a perfectly square channel. This is done by computing exactly the flow of a capsule in slightly rectangular channels and comparing the results with those obtained in square channels. It is found that, within a rectangular channel with an appropriately defined deviation from squareness of 5%, the capsule deformed profiles are close to those in a square channel, and that the inverse analysis procedure can be used