Compartmentalized microfluidic devices are designed to engineer the cellular environment for cell cultures. The practical use of the compartmentalized chambers can be expanded to induce co-pathological cell cultures, where one cell population expresses a specific disease state, while being in direct-cell or metabolic contact to a second or third unaffected cell population. A typical example for co-pathological cell states in the brain is the well-known neurodegenerative Alzheimer’s disease (AD), which still lacks effective treatment approaches. In the brain, AD shows specific disease progression patterns from one functional brain region to another. However, in normal dissociated neuron cultures using petri dishes, the extraction of the progression patterns is very difficult. In this chapter, we describe the methodology to design and fabricate a compartmentalized microfluidic device and apply it to an in vitro AD model to mimic the key pathological hallmarks of AD, allowing us to study disease progression patterns from a “diseased” towards a “healthy” cell population. This derived co-pathological model of AD provides the ability to monitor time-variant changes in cell network morphology and electrophysiology during disease progression and may potentially be used for pharmaceutical tests.