{ "background": "Rural clinic systems in Ethiopia are critical for healthcare delivery, yet robust methodologies for evaluating their clinical performance are underdeveloped. Existing assessments often fail to account for the hierarchical structure of patient data nested within clinics and regions, potentially leading to biased inferences.", "purpose and objectives": "This study aimed to methodologically evaluate the application of multilevel modelling for analysing clinical outcomes within these systems and to identify key facility-level factors influencing patient recovery rates.", "methodology": "We conducted a secondary analysis of anonymised longitudinal patient records from multiple rural clinics. A three-level random intercept logistic regression model was fitted to estimate the probability of successful treatment outcome. The model is specified as $\\logit(\\pi{ijk}) = \\beta0 + \\beta X{ijk} + uk + v{jk} + e{ijk}$, where $uk$ and $v{jk}$ are random effects for region and clinic, respectively, with robust standard errors used for inference.", "findings": "Clinic-level infrastructural readiness explained 22% of the variance in successful outcomes (95% CI: 15% to 29%). For each standard deviation increase in a clinic's drug availability score, the odds of patient recovery increased by 1.8 (95% CI: 1.5 to 2.2), after controlling for individual patient characteristics.", "conclusion": "Multilevel regression provides a statistically sound framework for evaluating clinical outcomes in hierarchically structured health systems, revealing that clinic-level resources are a significant determinant of patient success.", "recommendations": "Health system evaluations should routinely employ multilevel models to appropriately attribute variance. Policy should prioritise equitable distribution of essential medicines and clinic infrastructure to improve aggregate clinical outcomes.", "key words": "health systems evaluation, hierarchical modelling, mixed-effects models, healthcare access, resource allocation, sub-Saharan Africa", "contribution statement": "This paper provides a novel methodological demonstration of how variance partitioning in multilevel models can quantify the specific contribution of