Several studies have found associations of genes with atrial fibrillation (AF), including SCN5A-H558R. However, there are limited data of these associations among populations living at different altitudes. We investigated the relationship between the SCN5A-H558R polymorphism and AF in Tibetans living at different altitudes in Qinghai, China. General clinical and genotype data were obtained from 72 patients with AF and 109 non-AF (NAF) individuals at middle altitudes, and from 102 patients with AF and 143 NAF individuals at high altitudes. Multifactor logistic regression was performed to determine associations and AF risk factors. SCN5A-H558R genotypes differed significantly between the AF and NAF groups (P < .0125) and the G allele was an independent AF risk factor (P < .05) at both altitudes, with no significant differences according to altitude (P > .0125). At middle altitudes, age, red blood cell distribution width (RDW-SD), left atrial internal diameter (LAD), and G allele were independent AF risk factors. At high altitudes, age, smoking, hypertension, RDW-SD, free triiodothyronine, LAD, and G allele were independent AF risk factors (P < .05). The G allele of SCN5A-H558R might be an independent risk factor of AF both high and middle altitude, but there are some differences in other clinical risk factors of AF.