Rationale A functional polymorphism of the serotonin transporter gene (5‐HTTLPR) has previously been related to upper airway pathology, but its contribution to obstructive sleep apnea (OSA), a highly prevalent sleep disorder in older adults, remains unclear. Objectives We aimed to investigate the relationship between apnea–hypopnea index (AHI) and genetic variations in the promoter region of the 5‐HTTLPR in older adults. Methods DNA samples from 94 community‐dwelling older adults (57% female, mean age 72 ± 8) were genotyped for the 5‐HTTLPR polymorphism. All participants were assessed in their homes with full ambulatory polysomnography in order to determine AHI and related parameters such as hypoxia, sleep fragmentation, and self‐reported daytime sleepiness. Results The 5‐HTT l allele was significantly associated with AHI (p = 0.019), with l allele carriers displaying a higher AHI than s allele homozygotes. A single allele change in 5‐HTTLPR genotype from s to l resulted in an increase of AHI by 4.46 per hour of sleep (95% CI, 0.75–8.17). The l allele was also associated with increased time during sleep spent at oxygen saturation levels below 90% (p = 0.014). Conclusions The observed significant association between the 5‐HTTLPR l allele and severity of OSA in older adults suggests that the l allele may be important to consider when assessing for OSA in this age group. This association may also explain some of the observed variability among serotonergic pharmacological treatment studies for OSA, and 5‐HTT genotype status may have to be taken into account in future therapeutic trials involving serotonergic agents. Copyright © 2013 John Wiley & Sons, Ltd.