This dissertation presents development of three-dimensional microelectrode arrays (3-D MEAs) for a variety of applications in the in-vitro and in-vivo arenas. MEAs are important tools for scientific discovery and medical advancement. Since MEAs can actively manipulate and monitor cellular activity at both the single cell and tissue levels, they provide extraordinary insight into complex electrogenic cellular interactions. MEAs are utilized for a wide range of applications: basic neural research, biosensors for chemical, biological and environmental detection of compounds, pharmacological screening, toxicology, prosthetic devices, cardiac pacing, epilepsy research and bioelectrodes. Planar or 2-D MEAs have been in existence for over 30 years but in order to study complex cellular network morphologies and tissue cultures (with 3-D network of electrogenic cells), 3-D MEAs are required. Current 3-D MEAs are based on silicon micromachining and/or complex assembly processes resulting in expensive manufacturing, questionable biocompatibility, and limited accessibility to end users. The 3-D MEAs developed in this work are polymer-based, thereby potentially enabling low cost mass manufacturing, biocompatibility and familiarity for end users of this technology---biologists, chemists, doctors and pharmacologists. This research begins with the development of laser micromachining based 3-D MEAs. Lasers are ideal for 3-D fabrication as they can machine material with substantial topographies in a non-contact manner. In order to develop 3-D MEAs, high aspect ratio micro-towers were fabricated using a double-side exposure technology of a negative tone epoxy-composite called SU-8. These tower arrays were then coated with a metal layer and a conformal polymer that was micromachined selectively with a laser in both 2-D and 3-D to create a mold. Metal was electrodeposited on this mold to create the MEAs. These MEAs were packaged and then evaluated electrically utilizing impedance spectroscopy and baseline noise measurements. 3-D cortical co-cultures of neurons and astrocytes were grown on these MEAs and excellent biocompatibility was demonstrated for up to 21 days in-vitro. For a true extension to a manufacturing process, a metal transfer micromolding based technique was developed to fabricate 3-D MEAs. The MEA master structures were fabricated using advanced mold fabrication technologies including inclined rotational exposure of SU-8 and micromolding. Two separate techniques were developed for selective metallization of micromolds---a shadow mask approach and an intentionally formed non-planar mold approach. Both these techniques enable self-aligned metal patterning in highly non-planar topographies without the need for complex, expensive and non-repeatable 3-D lithography processes. 3-D MEAs were micromolded from these metalized molds multiple times. Simple packaging technologies were developed to accommodate the MEA in a footprint compatible with commercial test setups. 2-D cortical cultures of neurons were grown on the MEAs for up to 5 days in-vitro to demonstrate biocompatibility of the materials used in MEA fabrication. Acute tissue slice electrophysiology was performed to demonstrate biological functionality. Analytical models were developed for the electrode impedance, baseline noise and shape prediction of molds. Process changes were developed to improve the yield of microelectrodes on the MEAs. The application of these MEAs was demonstrated in an in-vitro arena for nerve tracking. The design, fabrication and packaging processes were modified to fit the desired application. Characterization of master structure sharpening techniques was...