The present invention provides methods for accurately classifying whether a sample from an individual is associated with an intestinal disorder. In particular, the present invention is useful for associating a sample from an individual as an IBS sample or as a non-IBS sample. The present invention is also useful for ruling out one or more diseases or disorders that present with IBS-like symptoms and ruling in IBS using statistical algorithms and/or empirical data. Thus, the present invention provides an accurate diagnostic prediction of an intestinal disorder and prognostic information useful for guiding treatment decisions.