The identification of plant-wide faults is a very important topic as it enables plant operators to decrease rejections or to increase the product quality. This paper shows a fault propagation approach for this field of interest based on time delay estimation. Due to the fact that the estimation of time delays in multiple-input single-output systems or nonlinear systems is either impossible or very difficult with known methods, a new method based on k nearest neighbor imputation was developed and is validated in this paper theoretically. The effectiveness of the identification algorithm is demonstrated on several simulations and on an industrial hydrocracker plant. (C) 2012 Elsevier Ltd. All rights reserved.