ObjectiveTo (1) examine the burden of multiple chronic conditions (MCC) in an urban health system, and (2) propose a methodology to identify subpopulations of interest based on diagnosis groups and costs.DesignRetrospective cross-sectional study.SettingMount Sinai Health System, set in all five boroughs of New York City, USA.Participants192 085 adult (18+) plan members of capitated Medicaid contracts between the Healthfirst managed care organisation and the Mount Sinai Health System in the years 2012 to 2014.MethodsWe classified adults as having 0, 1, 2, 3, 4 or 5+ chronic conditions from a list of 69 chronic conditions. After summarising the demographics, geography and prevalence of MCC within this population, we then described groups of patients (segments) using a novel methodology: we combinatorially defined 18 768 potential segments of patients by a pair of chronic conditions, a sex and an age group, and then ranked segments by (1) frequency, (2) cost and (3) ratios of observed to expected frequencies of co-occurring chronic conditions. We then compiled pairs of conditions that occur more frequently together than otherwise expected.Results61.5% of the study population suffers from two or more chronic conditions. The most frequent dyad was hypertension and hyperlipidaemia (19%) and the most frequent triad was diabetes, hypertension and hyperlipidaemia (10%). Women aged 50 to 65 with hypertension and hyperlipidaemia were the leading cost segment in the study population. Costs and prevalence of MCC increase with number of conditions and age. The disease dyads associated with the largest observed/expected ratios were pulmonary disease and myocardial infarction. Inter-borough range MCC prevalence was 16%.ConclusionsIn this low-income, urban population, MCC is more prevalent (61%) than nationally (42%), motivating further research and intervention in this population. By identifying potential target populations in an interpretable manner, this segmenting methodology has utility for health services analysts.