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Jonathan Mark Ellen, M.D.

Photo of Dr. Jonathan Mark Ellen, M.D.

President, Johns Hopkins All Children's Hospital

Professor of Pediatrics


Expertise: Adolescent Medicine, General Pediatrics, Pediatrics

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Johns Hopkins Pediatrics
Appointment Phone: 443-997-5437

200 N. Wolfe Street
Rubenstein Child Health Building
Baltimore, MD 21287 map
Phone: 410-550-4115
Fax: 410-502-5440


Dr. Jonathan Ellen is a professor of pediatrics at the Johns Hopkins University School of Medicine and a professor in the Department of Epidemiology and the Department of Population, Family and Reproductive Health in the Johns Hopkins Bloomberg School of Public Health.

Dr. Ellen serves as president and vice dean of Johns Hopkins All Children's Hospital.

After graduating from the University of Pennsylvania, he received his medical degree from Temple University and completed an internship and residency in pediatrics at Children’s Hospital of Philadelphia. Dr. Ellen completed a fellowship in adolescent medicine at the University of California, San Francisco (UCSF), followed by fellowships in sexually transmitted diseases at UCSF, the San Francisco Department of Public Health, and the Centers for Disease Control and Prevention. He joined the Johns Hopkins faculty in 1999. 

Dr. Ellen was named vice dean for Johns Hopkins All Children's Hospital in 2011 and president of Johns Hopkins All Children's Hospital in 2012. Previously, he led the Center for Child and Community Health at Johns Hopkins and was director of the Department of Pediatrics and Neonatology at Johns Hopkins Bayview Medical Center. 

His research focuses on the prevention of sexually transmitted infections (STIs) in adolescents, including HIV, and the factors associated with the acquisition, screening, treatment and care of these infections. He has served as a consultant to the Baltimore City Health Department, the San Francisco Department of Health, the Centers for Disease Control and Prevention (CDC), the U.S. Department of Health and Human Services, the National Academy of Sciences and the White House Office of National AIDS Policy. 

Dr. Ellen is certified in Adolescent Medicine by the American Board of Pediatrics and in Pediatrics by the American Board of Pediatrics. He has trained more than 40 pre- and post-doctoral fellows in adolescent medicine and public health and authored more than 175 peer-reviewed scientific articles along with 30 reviews, editorials and book chapters. more


  • President, Johns Hopkins All Children's Hospital
  • Vice Dean, Johns Hopkins All Children's Hospital
  • Professor of Pediatrics



  • MD, Temple University School of Medicine (1988)


  • The Children's Hospital of Philadelphia / Pediatrics (1991)


  • University of California San Francisco / Adolescent Medicine (1995)

Board Certifications

  • American Board of Pediatrics / Adolescent Medicine (1994)
  • American Board of Pediatrics / Pediatrics (1991)

Research & Publications

Research Summary

Dr. Ellen’s research focuses on community-based health initiatives, especially structural changes to impact asthma, obesity and infant mortality. He was previously the leader of the Adolescent Medicine Trials Network for HIV/AIDS Intervention, serving as principal investigator for Connect to Protect®, a community coalition-based program.

His past research focused on preventing sexually transmitted infections, including HIV, in adolescents and the structural and environmental factors associated with disease transmission, and he received more than $25 million in research awards from the CDC, NIH and other agencies.

Selected Publications

View all on Pubmed

Chutuape KS, Muyeed AZ, Willard N, Greenberg L, Ellen JM; the Adolescent Medicine Trials Network for HIV/AIDS Interventions. "Adding to the HIV Prevention Portfolio - the Achievement of Structural Changes by 13 Connect to Protect® Coalitions." Glob J Community Psychol Pract. 2014;5(2):1-8.

Lee L, Rand CS, Ellen JM, Agwu AL. "Further thoughts on starting antiretroviral therapy: a response to ball." J Adolesc Health. 2015 Feb;56(2):254. doi: 10.1016/j.jadohealth.2014.11.006.

Ellen JM, Greenberg L, Willard N, Stines S, Korelitz J, Boyer CB; and the Adolescent Medicine Trials Network for HIV/AIDS Interventions. "Cross-sectional survey comparing HIV risk behaviours of adolescent and young adult men who have sex with men only and men who have sex with men and women in the US and Puerto Rico." Sex Transm Infect. 2015 Jan 13.

Ellen JM, Greenberg L, Willard N, Korelitz J, Kapogiannis BG, Monte D, Boyer CB, Harper GW, Henry-Reid LM, Friedman LB, Gonin R. "Evaluation of the Effect of Human Immunodeficiency Virus-Related Structural Interventions: The Connect to Protect Project." JAMA Pediatr. 2015 Jan 12. doi: 10.1001/jamapediatrics.2014.3010. [Epub ahead of print]

Decker MR, Rodney R, Chung SE, Jennings JM, Ellen JM, Sherman SG. "HIV testing among youth in a high-risk city: prevalence, predictors, and gender differences." AIDS Care. 2014 Dec 12:1-6. [Epub ahead of print]

Videos & Media

This Month at All Children's Hospital - November 2010

This Month at All Children's, February 2011

Jonathan Ellen, MD talks about the Future of Care

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