Abstract In this paper we analyze a class of state space identification algorithms for time-series, based on canonical correlation analysis, in the light of recent results on stochastic systems theory. In principle, these so called “subspace methods” can be described as covariance estimation followed by stochastic realization. The methods offer the major advantage of converting the nonlinear parameter estimation phase in traditional ARMA models identification into the solution of a Riccati equation but introduce at the same time some nontrivial mathematical problems related to positivity. The reason for this is that an essential part of the problem is equivalent to the well-known rational covariance extension problem. Therefore, the usual deterministic arguments based on factorization of a Hankel matrix are not valid for generic data, something that is habitually overlooked in the literature. We demonstrate that there is no guarantee that several popular identification procedures based on the same principle will not fail to produce a positive extension, unless some rather stringent assumptions are made which, in general, are not explicitly reported. In this paper the statistical problem of stochastic modeling from estimated covariances is phrased in the geometric language of stochastic realization theory. We review the basic ideas of stochastic realization theory in the context of identification, discuss the concept of stochastic balancing and of stochastic model reduction by principal subsystem truncation. The model reduction method of Desai and Pal (1982) [A realization approach to stochastic model reduction. Proc. 1 st Decision and Control Conf., pp. 1105–1112.], based on truncated balanced stochastic realizations, is partially justified, showing that the reduced system structure has a positive covariance sequence but is in general not balanced. As a byproduct of this analysis we obtain a theorem prescribing conditions under which the ‘subspace identification’ methods produce bona fide stochastic systems.