PurposeMultimorbidity [defined as two or more long-term conditions (LTCs)] contributes to increased treatment and medication burden, poor health-related quality of life, and worse outcomes. Management strategies need to be patient centred and tailored depending on existing comorbidities; however, little is known about the prevalence and patterns of comorbidities in people with chronic kidney disease (CKD). We investigated the prevalence of multimorbidity and comorbidity patterns across all CKD stages.MethodsMultimorbidity was assessed, using a composite of self-report and clinical data, across four CKD groups stratified by eGFR [stage 1–2, stage 3a&b, stage 4–5, and kidney transplant (KTx)]. Principal component analysis using varimax rotation was used to identify comorbidity clusters across each group.ResultsOf the 978 participants (mean 66.3 ± 14 years, 60% male), 96.0% had multimorbidity. In addition to CKD, the mean number of comorbidities was 3.0 ± 1.7. Complex multimorbidity (i.e. ≥ 4 multiple LTCs) was identified in 560 (57.3%) participants. When stratified by CKD stage, the two most prevalent comorbidities across all stages were hypertension (> 55%) and musculoskeletal disorders (> 40%). The next most prevalent comorbidity for CKD stages 1–2 was lung conditions and for CKD stages 3 and 4–5 it was heart problems. CKD stages 1–2 showed different comorbidity patterns and clustering compared to other CKD stages.ConclusionMost people across the spectrum of CKD have multimorbidity. Different patterns of multimorbidity exist at different stages of CKD, and as such, clinicians should consider patient comorbidities to integrate care and provide effective treatment strategies.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11255-023-03516-1.