Chronic kidney disease (CKD) is commonly comorbid with hypertension, diabetes, and cardiovascular disease (CVD). However, the extent of comorbidity in CKD across a range of concordant (shared pathophysiology and/or treatment) conditions and discordant (unrelated pathophysiology and/or different or contradictory treatment) conditions is not well documented. To ascertain the prevalence of comorbidity, across 39 physical and mental health comorbidities, in adults with CKD in a large, nationally representative primary care population. Cross-sectional analysis of a primary care dataset representing 1 274 374 adults in Scotland. This study was a secondary analysis of general practice electronic medical record data using binary logistic regression models adjusted for age, sex, and socioeconomic status. Data of adults aged ≥25 years and 40 long-term conditions were used. A total of 98.2% of adults with CKD had at least one comorbidity, versus 51.8% in controls. After adjustment for age, sex, and deprivation, people with CKD were more likely to have 1 (adjusted odds ratio aOR 6.5, 95% confidence interval CI = 6.0 to 7.1), 2-3 (aOR 15.2, 95% CI = 14.0 to 16.5), 4-6 (odds ratio OR 26.6, 95% CI = 24.4 to 28.9), and ≥7 other conditions (OR 41.9, 95% CI = 38.3 to 45.8). Furthermore, all concordant (seven out of seven), the majority of discordant physical health conditions (17 out of 24), and mental health conditions (six out of eight) had statistically significant positive associations with CKD after adjustment. Chronic kidney disease is associated with extreme comorbidity across a wide range of mental and physical conditions. Routine care for people with CKD should include recognition and management of comorbidities, and clinical guidelines should support clinicians to do this.