Parkinson's Disease is the second most common neurodegenerative disorder worldwide, with growing numbers and considerable societal and economic concerns. Human cell culture systems are efficient models for neurodegenerative disorders and allow for personalized, non-invasive analysis of cellular and molecular disease mechanisms. Midbrain organoids and assembloids are advanced 3D culture systems that recapitulate the human midbrain, which is highly affected by Parkinson's disease. Here, we used healthy control and patient-specific midbrain assembloids to assess mitochondrial DNA phenotypes and NfL levels alongside neurodegeneration and alpha-synuclein phosphorylation. Importantly, alterations in mitochondrial DNA homeostasis and NfL levels can be assayed in the supernatant and therefore are particularly suitable as biomarkers and for high throughput screening approaches.