Background <p>Epigenetic modification of the <i>APOL1</i> gene carrying risk alleles (G1 and G2) may represent a therapeutic strategy for <i>APOL1</i>-related kidney diseases. However, DNA methylation changes associated with <i>APOL1</i> have not been thoroughly characterized.</p> Methods <p>We conducted an epigenome-wide association study (EWAS) of <i>APOL1</i> risk alleles in 399 African Americans with chronic kidney disease (CKD) from the Atherosclerosis Risk in Communities (ARIC) study cohort using blood DNA samples. These associations were further examined in 1,677 African Americans with preserved kidney function. Additionally, the relationships between the identified CpGs and the expression of <i>APOL1</i> and nearby genes were evaluated in normal kidney tissue. <i>APOL1</i> risk–associated CpGs were tested for associations with estimated glomerular filtration rate based on creatinine and cystatin C (eGFR_crcys) and with urine albumin-to-creatinine ratio (ACR). Methylation patterns were additionally assessed for differentially methylated regions and associations with kidney function. We further evaluated whether <i>APOL1</i> risk-associated CpGs can modulate the relationship between <i>APOL1</i> risk alleles and kidney function measures.</p> Results <p>Four CpGs (cg15716373, cg16528833, cg21032535, and cg14589586) were significantly associated with <i>APOL1</i> risk alleles, mapping to two enhancers and two promoters within the <i>APOL1-APOL4-MYH9</i> region. Among <i>APOL1</i> high-risk carriers, cg14589586 in the <i>APOL2</i> promoter was inversely correlated with cg15716373 in an <i>APOL1</i> intron, a pattern absent in White Americans. The association between the four CpGs and <i>APOL1</i> risk alleles was also present among participants with preserved kidney function. In normal kidney tissue, cg14589586 and cg16528833 were significantly associated with the expression levels of multiple genes in this region, including <i>APOL1</i> and <i>MYH9</i>. Multiple CpGs located within the <i>APOL1-APOL4-MYH9</i> region exhibited significant joint associations with eGFR_crcys and ACR. <i>APOL1</i> risk-associated CpGs showed significant interactions with APOL1 risk alleles in relation to kidney function.</p> Conclusion <p><i>APOL1</i> risk alleles are associated with complex DNA methylation alterations across the <i>APOL1-APOL4-MYH9</i> region, potentially regulating multiple genes within this locus. APOL1 risk–associated CpGs may represent therapeutic targets for <i>APOL1</i>-related kidney diseases.</p>