Background and purpose Extracranial internal carotid artery thromboembolism is one major cause of ischaemic stroke and the predictive value of non-high-density lipoprotein cholesterol (non-HDLC) is superior to low-density lipoprotein cholesterol (LDLC). This study aimed to assess the association between non-HDLC levels and the prevalence of asymptomatic extracranial internal carotid artery stenosis (EICAS) as well as the predictive value of non-HDLC over LDLC on EICAS presence. Methods The Asymptomatic Polyvascular Abnormalities Community study is a subset of the Kailuan study emphasizing asymptomatic polyvascular abnormalities in Chinese adults. A total of 5351 participants, aged >= 40, without history of cardiovascular disease were enrolled in this study. Carotid duplex ultrasonography was carried out for the detection of EICAS. Results Of the 5351 patients, 2.5% (131/5351) were diagnosed with EICAS (stenosis >= 50%). Univariate analysis showed that non-HDLC is an independent indicator for asymptomatic EICAS [odds ratio (OR) 1.49, 95% confidence interval (CI) 1.17-1.91]; the same result was reached in multivariate analysis after adjustment for confounding factors (OR 1.32, 95% CI 1.00-1.75), especially for people with hypertension (OR 1.52, 95% CI 1.11-2.08), whilst non-HDLC failed to show better predictive value of EICAS than LDLC (OR 1.45, 95% CI 1.02-2.05). Conclusions Non-HDLC is an independent risk factor for EICAS prevalence, especially for hypertension patients. Although the predictive value of non-HDLC was no better than LDLC on EICAS presence, non-HDLC is still a powerful atherogenic factor and potential therapeutic target for EICAS.