Two multi-story atriums connect the lab floors and provide a visual connection and gathering space for the staff. Common functions such as conference rooms and a library are located off of this space on all floors. The building also includes a large cafeteria which doubles as a meeting space, and a seminar room for scientific conferences. Each floor includes break rooms and extra corridor space for informal meetings.

The interior fit-up changes Millennium's office culture from closed, private offices to open, flexible work spaces. The intention is to promote the "cross pollination" of ideas in a variety of disciplines and collaboration among scientists, executives, and staff. There are two workspace standards: 10' x 15' (for senior staff offices and shared two-person offices) and 10' x 10' (for single occupancy).

Biology and chemistry laboratories, where researchers work most intensely, are located on the exterior. Labs are designed on a 10'-6" x 45' module including bench space, an equipment zone within the lab, and a separate zone for isolated support rooms such as dark rooms, cold rooms, and hot labs. All labs are designed generically to accommodate the rapidly changing nature of Millennium's research.

The labs house genomics-based research into specific disease targets for pharmaceutical research and basic research into the genetic engineering and structure of disease mechanisms for atherosclerosis, obesity, diabetes, central nervous system conditions, and others, along with drug discovery, drug assay, compound screening, gene sequencing, robotic screening, nuclear magnetic resonance (NMR) imaging, and extensive mass spectrometry.