To date, PHMR has often relied on male/female stratification, but rarely considers the complex, intersecting social positions of men and women in describing the prevalence of health and disease. Stratification on an Intersectional Gender-Score (IG-Score), which is based on a variety of social covariables, would allow comparison of the prevalence of individuals who share the same complex intersectional profile (IG-Score). The cross-sectional case study was based on the German Socio-Economic Panel 2017 (n = 23,269 age 18+). After stratification, covariable-balance within the total sample and IG-Score-subgroups was assessed by standardized mean differences. Prevalence of self-rated health, mental distress, depression and hypertension was compared in men and women. In the IG-Score-subgroup with highest proportion of males and lowest probability of falling into the ‘woman’-category, most individuals were in full-time employment. The IG-Score-subgroup with highest proportion of women and highest probability of falling into the ‘woman’-category was characterized by part-time/occasional employment, housewife/-husband, and maternity/parental leave. Gender differences in prevalence of health indicators remained within the male-dominated IG-Score-subgroup, whereas the same prevalence of depression and self-rated health was observed for men and women constituting the female-dominated IG-Score-subgroup. These results might indicate that sex/gender differences of depression and self-rated health could be interpreted against the background of gender associated processes. In summary, the proposed procedure allows comparison of prevalence of health indicators conditional on men and women sharing the same complex intersectional profile.