In 2002, Lincoln was certified as a Designated AIDS Center by the New York State Department of Health in recognition of the high quality and broad range of services offered to patients. Lincoln's Department of HIV Services provides patients with culturally competent, comprehensive HIV services. Services include, but are not limited to, primary HIV health care, psychological evaluations, individual supportive counseling and testing, case management, client advocacy with outside agencies, home visits, partner notification assistance, domestic violence assistance, and collaboration with client service providers among other services.

Through collaboration with the Bronx Families and Adolescent Children Consortium, Lincoln offers competent family and youth centered services that include HIV pre and post test counseling adolescent support groups, after school programs, health education workshops, developmental and cognitive assessments, legal advocacy, case findings and linkages to research for children, adolescents, women and families in the Bronx.

Lincoln also conducts outreach by trained public health workers who conduct workshops and provide education about HIV/AIDS, including how to prevent transmission of the virus to others, and offers referrals to medical and psychosocial services for those who test positive for the virus.

HIV counseling and testing is available Mondays through Fridays through self-referrals or a referral from a Lincoln Hospital physician.