Health care for the nation's horse population entered a new era on June 7, 2000, when the Mary Anne McPhail Equine Performance Center officially opened. The 18,000-square-foot building expanded the College's facilities for clinical evaluations and research studies of equine health problems.

The university approved a new graduate program in comparative medicine and integrative biology in the College of Veterinary Medicine, effective May 21, 2001.

On July 26, 2001, the Vet School Confidential world premiere was held at the Wharton Center's Pasant Theater. Rocket Pictures had spent over a year filming at the College. The 13-episode series began showing on the Animal Planet Network in August.

On September 12, 2001, a ceremony celebrated the new Animal Health Diagnostic Laboratory ground breaking. The building was completed in 2004 and renamed the Diagnostic Center for Population and Animal Health.

The new Biomedical and Physical Sciences Building was officially opened on April 12, 2002. The building became the home of MSU's Departments of Microbiology and Molecular Genetics (now named Microbiology, Genetics, & Immunology), Physiology, and Physics and Astronomy, as well as several MSU interdisciplinary centers and projects.

A new critical care unit opened on May 29, 2002, in the Veterinary Teaching Hospital's Small Animal Clinic.

MSU Diagnostic Center for Population and Animal Health conducted a record-setting 1.1 million tests in 2002.

In March 2003, Dr. Patrick LeBlanc, a board-certified veterinary anesthesiologist who was a tenured faculty member at MSU from 1986-1994, returned to MSU as the director of what was then named the MSU Veterinary Teaching Hospital.

On December 12, 2003, the first Celebration of Life event was held, which reunited patients—mainly dogs and cats—who were treated at MSU's Veterinary Medical Center with the veterinarians and veterinary technicians who care for them.

A diverse group of more than 100 participants, representing faculty, staff, students, alumni, and other stakeholders, met in December 2003 to discuss the College's future. In conjunction with that, approximately 95 people associated with the college participated in a four-month long leadership development program.

Dr. Lorraine Sordillo joined the faculty in January 2004 as the first holder of the Meadow Brook Endowed Chair in Farm Animal Health and Well-being.

In June 2004, the Institute for Environmental Toxicology was renamed the Center for Integrative Toxicology. The center took on a new, expanded mission, which warranted a new name.

On September 20, 2004 the new Diagnostic Center for Population and Animal Health opened.

Construction began on the College's new Center for Comparative Oncology in 2004, with the goal of providing improved treatments and eventual cures for cancer.

Construction began in January 2005 for the Matilda R. Wilson Pegasus Critical Care Center that would provide much-needed care for horses and other large animals with infectious diseases, and also provide teaching and research opportunities for faculty and students in an approximately 9,0000 square foot-facility.

The Advanced Rehabilitation Center was opened in the Veterinary Teaching Hospital's Small Animal Clinic in February 2005.

Also in February 2005, Dean Lonnie King began a year with the Centers for Disease Control and Prevention in Atlanta serving as the director of the agency's new Office of Strategy and Innovation. King had been consulting with the CDC's National Center for Infectious Diseases since 2004 on strategic planning and work force planning, as well as helping them build capacity in veterinary medicine and animal health.

A grand opening ceremony for the Matilda R. Wilson Pegasus Critical Care Center was held in September 2005 and a ceremony was held in late October 2005 for the College's new Animal Cancer Care Clinic, the first phase of the college's planned Center for Comparative Oncology.

A new Learning and Assessment Center to aid health professions students opened on March 16, 2006. The center, located at A-610 East Fee Hall was designed to help health professions students improve their communication and diagnostic skills. The MSU College of Veterinary Medicine was part of a multi-college effort at MSU that established the center. Other participants were the Colleges of Human Medicine, Nursing, and Osteopathic Medicine, along with the Medical Technology Program, which is housed in the College of Natural Science.

Dean Lonnie King stepped down as dean on June 30, 2006. He assumed the role as the first director of the new National Center for Zoonoses, Vector-Borne, and Enteric Diseases at the Centers for Disease Control in Atlanta, Georgia.

Dr. Christopher Brown accepted the offer to become the next dean of the College of Veterinary Medicine. He officially began his role as dean on September 1, 2006. In the interim, Dr. Charles DeCamp, chair of the Department of Small Animal Clinical Sciences, served as acting dean. Brown had been at the College previously as a faculty member in large-animal clinical sciences from 1979 to 1994.

Dr. John Baker took over the Dean position on June 20, 2014. Baker has been the section head for Food Animal Medicine and Surgery in Large Animal Clinical Sciences, the associate director of AgBioResearch, associate dean for research and graduate studies within AgBioResearch, and is also board certified by the American College of Veterinary Internal Medicine.