Atorvastatin is the most prescribed 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor used to lower cardiovascular risk and constitutes one of the best-selling drugs world-wide. Several physiologically based pharmacokinetic (PBPK) models have been developed to assess its non-straightforward pharmacokinetics (PK) as well as that of its metabolites and have been only applied to assess drug-drug interactions (DDI). Here we present a full PBPK model for atorvastatin and its metabolites able to predict within a 2-fold error their PK after the administration of a solid oral dosage form containing the calcium salt of atorvastatin in single and multiple dosing schedules at 20, 40, and 80 mg and 10 mg dose levels, respectively. Internal validation with data from Phase 1 clinical trials as well as external validation in predicting clinically relevant DDIs consolidated model structure and parameterization. The model has been used to quantitatively assess the drug-gene interaction (DGI) between SLCO1B1 polymorphisms and atorvastatin exposure and revealed that patients with a reduced activity in hepatic uptake of atorvastatin are at increased risk of suffering muscle discomfort because of a 30% lower clearance (p < 0.01), leading to a 40% and 33% higher (p < 0.05) atorvastatin AUC and C_max, respectively. These findings could explain the reported hazard ratio of 1.4 (95% CI: 1.1–1.7, p = 0.02) for suffering statin-induced myopathies and the treatment discontinuation among these patients (odds ratio 1.67, p = 0.0001) observed in the context of routine clinical care.