Pharmacokinetic (PK) data often contain concentration measurements below the quantification limit (BQL). While specific values cannot be assigned to these observations, nevertheless these observed BQL data are informative and generally known to be lower than the lower limit of quantification (LLQ). Setting BQLs as missing data violates the usual missing at random (MAR) assumption applied to the statistical methods, and therefore leads to biased or less precise parameter estimation. By definition, these data lie within the interval [0, LLQ], and can be considered as censored observations. Statistical methods that handle censored data, such as maximum likelihood and Bayesian methods, are thus useful in the modelling of such data sets. The main aim of this work was to investigate the impact of the amount of BQL observations on the bias and precision of parameter estimates in population PK models (non-linear mixed effects models in general) under maximum likelihood method as implemented in SAS and NONMEM, and a Bayesian approach using Markov chain Monte Carlo (MCMC) as applied in WinBUGS. A second aim was to compare these different methods in dealing with BQL or censored data in a practical situation. The evaluation was illustrated by simulation based on a simple PK model, where a number of data sets were simulated from a one-compartment first-order elimination PK model. Several quantification limits were applied to each of the simulated data to generate data sets with certain amounts of BQL data. The average percentage of BQL ranged from 25% to 75%. Their influence on the bias and precision of all population PK model parameters such as clearance and volume distribution under each estimation approach was explored and compared. Copyright © 2009 John Wiley & Sons, Ltd.