Distributed watershed models are increasingly being used to support decisions about alternative management strategies in the areas of landuse change, climate change, water allocation, and pollution control. For this reason it is important that these models pass through a careful calibration and uncertainty analysis. Furthermore, as calibration model parameters are always conditional in nature the meaning of a calibrated model, its domain of use, and its uncertainty should be clear to both the analyst and the decision maker. Large-scale distributed models are particularly difficult to calibrate and to interpret the calibration because of large model uncertainty, input uncertainty, and parameter nonuniqueness. To perform calibration and uncertainty analysis, in recent years many procedures have become available. As only one technique cannot be applied to all situations and different projects can benefit from different procedures, we have linked, for the time being, three programs to the hydrologic simulator Soil and Water Assessment Tools (SWAT) (Arnold et al., 1998) under the same platform, SWAT-CUP (SWAT Calibration Uncertainty Procedures). These procedures include: Generalized Likelihood Uncertainty Estimation (GLUE) (Beven and Binley, 1992), Parameter Solution (ParaSol) (van Griensven and Meixner, 2006), and Sequential Uncertainty FItting (SUFI-2) (Abbaspour, et al., 2007). In this paper we describe SWAT-CUP and the three procedures and provide an application example using SUFI-2.