Clinical trial simulation (CTS) is a valuable tool in drug development. To obtain realistic scenarios, the subjects included in the CTS must be representative of the target population. Common ways of generating virtual subjects are based upon bootstrap (BS) procedures or multivariate normal distributions (MVND). Here, we investigated the performance of an alternative method based on multiple imputation (MI). Age, weight, serum creatinine, creatinine clearance, sex and race data from a hypertension drug development program were used. The methods were evaluated based on the original data set (internal evaluation) and on their ability to reproduce an older, unobserved population (extrapolation). Similar results were obtained in the internal evaluation in terms of summary statistics. However, BS was able to preserve the correlation structure of the empirical distribution, which was not adequately reproduced by MVND; MI was in between BS and MVND. BS does not allow to extrapolate to an unobserved population. Improved extrapolation performance of the continuous covariates was observed for MI over MVND, yet after removing the healthy subject data from the training data set, there was no clear difference between the methods. Sex was better predicted by MVND vs. MI, while similar results were obtained for race. If CTS is used to simulate within the range of the observed distribution, BS is the preferred method for covariates simulation. When extrapolating to new populations, a parametric method like MI/MVND is needed. As MVND rests on relatively strong assumptions, MI appears to be more robust when deviations from these assumptions occur.