A methodology is developed to analyze a multivariate linear model, which occurs in many geodetic and geophysical applications. Proper analysis of multivariate GPS coordinate time-series is considered to be an application. General, special, and more practical stochastic models are adopted to assess the noise characteristics of multivariate time-series. The least-squares variance component estimation (LS-VCE) is applied to estimate full covariance matrices among different series. For the special model, it is shown that the multivariate time-series can be estimated separately, and that the (cross) correlation between series propagates directly into the correlation between the corresponding parameters in the functional model. The time-series of five permanent GPS stations are used to show how the correlation between series propagates into the site velocities. The results subsequently conclude that the general model is close to the more practical model, for which an iterative algorithm is presented. The results also indicate that the correlation between series of different coordinate components per station is not significant. However, the spatial correlation between different stations for individual components is significant (a correlation of 0.9 over short baselines) both for white and for colored noise components.