IntroductionLiving in socioeconomic disadvantage has been conceptualised as a chronic stressor, although this contradicts evidence from studies using hair cortisol and cortisone as a measure of hypothalamus-pituitary-adrenal (HPA)11HPA axis: Hypothalamus Pituitary Adrenal axis axis activity. These studies used complete case analyses, ignoring the impact of missing data for inference, despite the high proportion of missing biomarker data. The methodological limitations of studies investigating the association between socioeconomic position (SEP)22SEP: Socio-economic Position defined as education, wealth, and social class and hair cortisol and cortisone are considered in this study by comparing three common methods to deal with missing data: (1) Complete Case Analysis (CCA),33CCA: Complete Case Analysis (2) Inverse Probability Weighting (IPW) 44IPW: Inverse Probability Weightingand (3) weighted Multiple Imputation (MI).55MI: Multiple Imputation This study examines if socioeconomic disadvantage is associated with higher levels of HPA axis activity as measured by hair cortisol and cortisone among older adults using three approaches for compensating for missing data. MethodCortisol and cortisone levels in hair samples from 4573 participants in the 6th wave (2012–2013) of the English Longitudinal Study of Ageing (ELSA)66ELSA: English Longitudinal Study of Ageing were examined, in relation to education, wealth, and social class. We compared linear regression models with CCA, weighted and multiple imputed weighted linear regression models. ResultsSocial groups with certain characteristics (i.e., ethnic minorities, in routine and manual occupations, physically inactive, with poorer health, and smokers) were less likely to have hair cortisol and hair cortisone data compared to the most advantaged groups. We found a consistent pattern of higher levels of hair cortisol and cortisone among the most socioeconomically disadvantaged groups compared to the most advantaged groups. Complete case approaches to missing data underestimated the levels of hair cortisol in education and social class and the levels of hair cortisone in education, wealth, and social class in the most disadvantaged groups. ConclusionThis study demonstrates that social disadvantage as measured by disadvantaged SEP is associated with increased HPA axis activity. The conceptualisation of social disadvantage as a chronic stressor may be valid and previous studies reporting no associations between SEP and hair cortisol may be biased due to their lack of consideration of missing data cases which showed the underrepresentation of disadvantaged social groups in the analyses. Future analyses using biosocial data may need to consider and adjust for missing data.