This study aimed to map Colombia’s pharmacogenomic (PGx) landscape with respect to ancestry by combining all PharmGKB variant-drug annotations with local allele-frequency data, in order to measure clinically relevant differences among ancestral groups and identify gaps that limit fair access to precision medicine. We analyzed 4,462 PharmGKB variant annotations spanning 1994–2024, narrowing the dataset to 1,216 significant single-nucleotide polymorphisms (SNPs) reported in 552 studies. Allele frequencies were compiled for five Colombian populations: two largely African-descended (Palenque [PLQ], Chocó [CHG]) and three predominantly European-descended (ATQCES, ATQPGC, CLM) using the CÓDIGO database. Spearman correlation coefficients assessed similarities between population-specific PGx profiles, and SNPs with frequency differences exceeding 25 percentage points were cataloged. The global PGx literature is heavily skewed toward European ancestry, representing 51.5% of 651,532 participants, while African ancestry accounted for only 0.46% (n = 3,031). European-leaning Antioquian populations showed strong internal correlations (r² ≥ 0.90), whereas PLQ displayed weak or inverse correlations with these groups (r² = −0.20 to −0.02) and only minimal similarity with CHG (r² = 0.12). Among the SNPs, 28 were highly frequent in PLQ (>75%) but uncommon in Europeans (<50%), while 44 exhibited the reverse pattern. Notable examples include CYP3A4 rs3735451-C (rivaroxaban; 87.1% vs. 23.2%), CYP3A5 rs776746-T (tacrolimus; 85% vs. 23.5%), and rs55881666-C (duloxetine; 15% vs. 84%). Globally, 71.5% of PGx studies originated in high-income nations. The substantial allele-frequency disparities and pronounced research biases underscore the need for ancestry-informed PGx testing and locally tailored dosing strategies in Colombia, while the study’s analytic framework and variant catalog provide a foundation for implementing precision pharmacotherapy in Latin-American admixed populations.
