In a genome‐wide association study of atorvastatin pharmacokinetics in 158 healthy volunteers, the SLCO1B1 c.521T>C (rs4149056) variant associated with increased area under the plasma concentration‐time curve from time zero to infinity (AUC0–∞) of atorvastatin (P = 1.2 × 10−10), 2‐hydroxy atorvastatin (P = 4.0 × 10−8), and 4‐hydroxy atorvastatin (P = 2.9 × 10−8). An intronic LPP variant, rs1975991, associated with reduced atorvastatin lactone AUC0–∞ (P = 3.8 × 10−8). Three UGT1A variants linked with UGT1A3*2 associated with increased 2‐hydroxy atorvastatin lactone AUC0–∞ (P = 3.9 × 10−8). Furthermore, a candidate gene analysis including 243 participants suggested that increased function SLCO1B1 variants and decreased activity CYP3A4 variants affect atorvastatin pharmacokinetics. Compared with individuals with normal function SLCO1B1 genotype, atorvastatin AUC0–∞ was 145% (90% confidence interval: 98‐203%; P = 5.6 × 10−11) larger in individuals with poor function, 24% (9‐41%; P = 0.0053) larger in those with decreased function, and 41% (16‐59%; P = 0.016) smaller in those with highly increased function SLCO1B1 genotype. Individuals with intermediate metabolizer CYP3A4 genotype (CYP3A4*2 or CYP3A4*22 heterozygotes) had 33% (14‐55%; P = 0.022) larger atorvastatin AUC0–∞ than those with normal metabolizer genotype. UGT1A3*2 heterozygotes had 16% (5‐25%; P = 0.017) smaller and LPP rs1975991 homozygotes had 34% (22‐44%; P = 4.8 × 10−5) smaller atorvastatin AUC0‐∞ than noncarriers. These data demonstrate that genetic variation in SLCO1B1, UGT1A3, LPP, and CYP3A4 affects atorvastatin pharmacokinetics. This is the first study to suggest that LPP rs1975991 may reduce atorvastatin exposure. Correction added on 6 April, after first online publication: An incomplete sentence (“= 0.017) smaller in heterozygotes for UGT1A3*2 and 34% (22%, 44%; P × 10−5) smaller in homozygotes for LPP noncarriers.”) has been corrected in this version.