The human breast cancer resistance protein (BCRP/ABCG2) is an ATP-binding cassette efflux transporter that uses ATP hydrolysis to expel xenobiotics from cells, including anti-cancer medications. It is expressed in the gastrointestinal tract, liver, kidney, and brain endothelium. Thus, ABCG2 functions as a tissue barrier to drug transport that strongly influences the pharmacokinetics of substrate medications. Genetic polymorphisms of ABCG2 are closely related to inter-individual variations in therapeutic performance. The common single nucleotide polymorphism c.421C>A, p.Q141K reduces cell surface expression of ABCG2 protein, resulting in lower efflux of substrates. Consequently, a higher plasma concentration of substrate is observed in patients carrying an ABCG2 c.421C>A allele. Detailed pharmacokinetic analyses have revealed that altered intestinal absorption is responsible for the distinct pharmacokinetics of ABCG2 substrates in genetic carriers of the ABCG2 c.421C>A polymorphism. Recent studies have focused on the high-alert medications among ABCG2 substrates (defined as those with high risk of adverse events), such as tyrosine kinase inhibitors (TKIs) and direct oral anti-coagulants (DOACs). For these high-alert medications, inter-individual variation may be closely related to the severity of side effects. In addition, ethnic differences in the frequency of ABCG2 c.421C>A have been reported, with markedly higher frequency in East Asian (˜30–60%) than Caucasian and African-American populations (˜5–10%). Therefore, ABCG2 polymorphisms must be considered not only in the drug development phase, but also in clinical practice. In the present review, we provide an update of basic and clinical knowledge on genetic polymorphisms of ABCG2.