Our findings can inform medical genetic studies. Introgressed Native American and African haplotypes in European Americans might have implications for studies of complex diseases, especially for diseases that vary in prevalence among ancestral populations, can produce subtle population structure that should be carefully controlled for in GWASs, and might impact the distribution of rare variants in studies of whole-genome sequence. Our results also suggest new avenues for research, such as the potential for including European Americans in admixture mapping.