Physiologically based pharmacokinetic (PBPK) models often include several sets of correlated parameters, such as organ volumes and blood flows. Because of recent advances in proteomics, it has been demonstrated that correlations are also present between abundances of drug-metabolising enzymes in the liver. As the focus of population PBPK has shifted the emphasis from the average individual to theoretically conceivable extremes, reliable estimation of the extreme cases has become paramount. We performed a simulation study to assess the impact of the correlation between the abundances of two enzymes on the pharmacokinetics of drugs that are substrate of both, under assumptions of presence or lack of such correlations. We considered three semi-physiological models representing the cases of: (1) intravenously administered drugs metabolised by two enzymes expressed in the liver; (2) orally administered drugs metabolised by CYP3A4 expressed in the liver and gut wall; (3) intravenously administered drugs that are substrates of CYP3A4 and OATP1B1 in the liver. Finally, the impact of considering or ignoring correlation between enzymatic abundances on global sensitivity analysis (GSA) was investigated using variance based GSA on a reduced PBPK model for repaglinide, substrate of CYP3A4 and CYP2C8. Implementing such correlations can increase the confidence interval for population pharmacokinetic parameters (e.g., AUC, bioavailability) and impact the GSA results. Ignoring these correlations could lead to the generation of implausible parameters combinations and to an incorrect estimation of pharmacokinetic related parameters. Thus, known correlations should always be considered in building population PBPK models.