There is experimental evidence that the performance of standard subspace algorithms from the literature (e.g. the N4SID method) may be surprisingly poor in certain experimental conditions. This happens typically when the past signals (past inputs and outputs) and future input spaces are nearly parallel. In this paper we argue that the poor behavior may be attributed to a form of ill-conditioning of the underlying multiple regression problem, which may occur for nearly parallel regressors. An elementary error analysis of the subspace identification problem, shows that there are two main possible causes of ill-conditioning. The first has to do with near collinearity of the state and future input subspaces. The second has to do with the dynamical structure of the input signal and may roughly be attributed to "lack of excitation". Stochastic realization theory constitutes a natural setting for analyzing subspace identification methods. In this setting, we undertake a comparative study of three widely used subspace methods (N4SID, Robust N4SlD and PO-MOESP). The last two methods are proven to be essentially equivalent and the relative accuracy, regarding the estimation of the (A, C) parameters, is shown to be the same. (C) 2003 Elsevier Ltd. All rights reserved.