Background: Suicidal ideation (SI) is a common and serious clinical concern in people with major depressive disorder (MDD). Inconsistent evidence suggests that individuals with SI may have a lower measured intelligence quotient (IQ) than those without SI. The aims of this study were to examine SI prevalence and its associations with demographic, clinical variables and IQ in Chinese drug-naive MDD patients. Methods: 488 drug-naive Chinese Han patients (male: 203, 41.6%) meeting a DSM-IV diagnosis of MDD were enrolled in a cross-sectional study involving seven hospitals. All participants were asked to complete a series of questionnaires, which include information on socio-demographic and clinical variables. The Hamilton Depression Rating Scale (HAMD), Hamilton Anxiety Rating Scale (HAMA) and Brief Psychiatric Rating Scale (BPRS) were also administered. Verbal IQ (VIQ), performance IQ (PIQ) and full-scale IQ (FIQ) scores were measured using the Chinese version of the Wechsler Adult Intelligence Scale-III (WAIS-III). We categorized patients with SI based on a cut-off score of >= 3 on HAMD item 3. Results: An estimated prevalence 32.8% (160/488) of drug-naive MDD patients experienced SI during the current episode of illness. Patients with SI were more likely to be divorced (x(2) = 6.93, p = 0.031), male (x(2) = 6.04, p = 0.014), had higher severity of depression and anxiety symptoms (t = - 8.14, p < 0.001, t = - 3.28, p < 0.001, respectively), comorbid psychotic features (t = - 5.71, p < 0.001), and lower FIQ levels (t = - 4.21, p < 0.001), when compared to patients without SI. Using logistic regression analysis and adjusting for confounding variables, the following variables were independently associated with SI: divorced marital status compared to married (OR = 4.674, 95% CI: 1.676 similar to 13.036), severity of depression symptoms (OR = 1.312, 95% CI: 1.196 similar to 1.440), psychotic features (OR = 1.044; 1.012 similar to 1.077), and FIQ/PIQ levels which expressed in OR per SD increase in IQ score (OR = 0.740, 95% CI: 0.561 similar to 0.977; OR = 0.744, 95% CI: 0.557 similar to 0.994, respectively). Limitations: A cross-sectional study which did not assess the influence of severity of SI. Conclusions: The prevalence of SI in drug-naive Chinese patients with MDD is high, and associated with marital status, severity of depression, psychotic features and measured IQ. Further research is needed to further explore these and other potentially relevant risk factors which might affect clinical outcomes.