Alzheimer’s and Parkinson’s disease are neurodegenerative diseases that are becoming increasingly frequent in our aging society. Their impact on patients, caretakers and society is high because of their long duration and high costs of treatment and caretaking. Efforts to delay, cure, or prevent these diseases have so far be unsuccessful. This failure reflects our limited understanding of the processes that lead to the diseases. Alzheimer’s and Parkinson’s disease are characterized by protein aggregates that develop in the brains of patients. Although these aggregates play a central role in the disease, there is increasing evidence that other factors such as the immune system are involved as well. Genetic studies have indeed demonstrated that the immune system plays an important role as a cause for Alzheimer’s and Parkinson’s disease. Consequently, we now face the challenge to investigate the large number of identified risk genes for their relevance in the disease process. Therefore, we aim to systematically investigate genetic risk factors for Alzheimer’s and Parkinson’s disease for their role in protein aggregation and the immune response in human and mouse nerve and immune cells from the brain to identify their biological role in the disease onset and progression.