SLC22A1 is a hepatic plasma membrane transporter that transports a wide array of endogenous and xenobiotic molecules; however its impact on the physiology has been largely unexplored. Genome-wide association studies (GWASs) have revealed novel associations at the SLC22A1 locus for plasma acylcarnitine and low-density lipoprotein (LDL) cholesterol levels, suggesting previously unknown roles of SLC22A1 in the regulation of acylcarnitine and cholesterol metabolism. In this study, we aimed to investigate the molecular mechanism by which SLC22A1 and its variants alter plasma acylcarnitine and LDL cholesterol levels. To study the hepatic function of SLC22A1, we generated liver-specific knockout or overexpression mouse models of SLC22A1 and closely examined their acylcarnitine and lipid profiles. We confirmed that SLC22A1 deletion or overexpression in mice drastically alters systemic acylcarnitine profiles but has little effect on LDL cholesterol levels. We further performed a series of in vitro and in vivo kinetic assays and found that SLC22A1 exports short-chain acylcarnitines from the liver to the blood, regulating the systemic availability of hepatic carnitine species. Next, we sought to identify the causal variants of SLC22A1 for the genetic association with serum acylcarnitine levels. We refined the association signal by improving the imputation method and performed conditional analyses to dissect independent signals. By close examination of the linkage relationship, we found that the reduced-function coding variants of SLC22A1 are strongly associated with lower serum acylcarnitine levels, the direction of which is consistent with the efflux function of SLC22A1. We further performed liver allele-specific expression analysis to find potential regulatory variants of SLC22A1. We discovered a splice junction variant and further validated its effect on the splicing of SLC22A1 transcript. In conclusion, our studies elucidated the molecular mechanism of the GWAS association at the SLC22A1 locus for serum acylcarnitines. We demonstrated a novel function of SLC22A1 in hepatic acylcarnitine efflux and further determined the impacts of coding and non-coding variants of SLC22A1, providing a directionally consistent explanation for the observed genetic association. Our results illustrate that large-scale genetic association studies, when combined with careful experimental validation, can drive novel biological insights.