Modeling of high dimensional dynamic data is a challenging task. The high dimensionality problem in process data is usually accounted for using latent variable models. Probabilistic slow feature analysis (PSFA) is an example of such an approach that accounts for high dimensionality while simultaneously capturing the process dynamics. However, PSFA also suffers from a drawback that it cannot use output information when determining the latent slow features. To address this lacunae, extension of the PSFA by incorporating outputs, resulting in Input-Output PSFA (IOPSFA) is proposed. IOPSFA can use both input and output information for extracting latent variables. Hence, inferential models based on IOPSFA are expected to have better predictive ability. The efficacy of the proposed approach with an industrial and a laboratory scale soft sensing case studies that have both complete and incomplete output measurements is evaluated, respectively. (c) 2018 American Institute of Chemical Engineers AIChE J, 65: 964-979, 2019