Background Little is known about how smoking cessation practices in primary care differ for patients with coronary heart disease (CHD) who have different comorbidities. Aim To determine the association between different patterns of comorbidity and smoking rates and smoking cessation interventions in primary care for patients with CHD. Design and setting Cross-sectional study of 81 456 adults with CHD in primary care in Scotland. Method Details of eight concordant physical comorbidities, 23 discordant physical comorbidities, and eight mental health comorbidities were extracted from electronic health records between April 2006 and March 2007. Multilevel binary logistic regression models were constructed to determine the association between these patterns of comorbidity and smoking status, smoking cessation advice, and smoking cessation medication (nicotine replacement therapy) prescribed. Results The most deprived quintile had nearly three times higher odds of being current smokers than the least deprived (odds ratio [OR] 2.76; 95% confidence interval [CI] = 2.49 to 3.05). People with CHD and two or more mental health comorbidities had more than twice the odds of being current smokers than those with no mental health conditions (OR 2.11; 95% CI = 1.99 to 2.24). Despite this, those with two or more mental health comorbidities (OR 0.77; 95% CI = 0.61 to 0.98) were less likely to receive smoking cessation advice, but absolute differences were small. Conclusion Patterns of comorbidity are associated with variation in smoking status and the delivery of smoking cessation advice among people with CHD in primary care. Those from the most deprived areas and those with mental health problems are considerably more likely to be current smokers and require additional smoking cessation support.