Abstract Background Syndemics, the clustering of health and social issues, disproportionately affect marginalized communities. While prior research indicates sex-specific variations in syndemic vulnerability, current research often overlooks other sociodemographic characteristics and their interaction. An intersectionality-informed syndemic approach could offer more insights into the mechanisms in syndemic suffering, providing a deeper understanding and identifying groups most affected by structural inequalities. Methods Our study focused on adult residents in Leiden and The Hague, the Netherlands, registered at different general practices. Using existing routine health data linked with Central Bureau for Statistics information, we included adults who were registered with a general practitioner in 2018 and 2019, had a minimum of two registered health conditions documented by their general practitioner, lived in Leiden or The Hague, and were at least 18 years old in 2018. Results A total of 43340 adults were included for analyses. Distinct health condition clusters were observed within sex and age groups. Women experiences a broader range of health issues, often characterized by mental and psychosomatic symptoms like mood/anxiety disorders and abdominal complaints. Conversely, men exhibited a higher prevalence of specific physical conditions, including hypertension, diabetes, and cardiovascular diseases. Conclusions The findings align with previous research, suggesting the importance of further exploration into the role of intersectionality in syndemics. Currently, we are investigating the foundations of these disparities, including interaction analyses and Multilevel Analysis of Individual Heterogeneity and Discriminatory Accuracy (MAIHDA). Using MAIHDA, we will examine the relationship between intersectionality and syndemic vulnerability, quantifying intersecting factors (sex, ethnicity, SES) and exploring their impact at individual and group levels. Key messages • Understanding intersectionality in health disparities is crucial for addressing syndemic vulnerabilities. • Tailored interventions informed by intersectionality may promote equitable health outcomes.