In the context of linear state space models with known parameters, the Kalman filter (KF) generates best linear unbiased predictions of the underlying states together with their corresponding Prediction Mean Square Errors (PMSE). However, in practice, when the filter is run with the parameters substituted by consistent estimates, the corresponding PMSE do not take into account the parameter uncertainty. Consequently, they underestimate their true counterparts. In this paper, we propose two new bootstrap procedures to obtain PMSE of the unobserved states designed to incorporate this latter uncertainty. We show that the new bootstrap procedures have better finite sample properties than bootstrap alternatives and than procedures based on the asymptotic approximation of the parameter distribution. The proposed procedures are implemented for estimating the PMSE of several key unobservable US macroeconomic variables as the output gap, the Non-accelerating Inflation Rate of Unemployment (NAIRU), the long-run investment rate and the core inflation. We show that taking into account the parameter uncertainty may change their prediction intervals and, consequently, the conclusions about the utility of the NAIRU as a macroeconomic indicator for expansions and recessions. (C) 2011 Elsevier B.V. All rights reserved.