Amid mounting evidence of widespread problems within the U.S. Department of Veterans Affairs’ health care system, President Barack Obama accepted the resignation of Veterans Affairs Secretary Eric Shinseki today.

But Shinseki’s replacement will face an uphill battle. As The Center for Investigative Reporting’s Aaron Glantz has been reporting for years, many of the issues plaguing the VA are not new.

Beyond recent revelations of delays in care at VA hospitals across the country, here’s a look at some of the health care and veterans benefits scandals that erupted on Shinseki’s watch – many of which will continue to plague the agency after his departure.

1. A massive backlog of disability claims

As CIR revealed last March, the ranks of veterans waiting more than a year for their benefits grew more than 2,000 percent under Obama. Though the VA has continued to make progress on the backlog since our reporting, more work remains. As of May 19, there are more than 547,000 veterans waiting for an answer to their claims. You can explore our interactive map – updated with new data each week – to see just how many veterans are waiting in your area.

2. An epidemic of opiate prescriptions

Between 2001 and 2012, the number of opiate prescriptions given to veterans by VA doctors rose a shocking 270 percent, leading to overdoses and abuse. And a recent inspector general report detailed how the agency has systematically failed to follow its own rules governing the prescription of addictive narcotic painkillers. Our interactive map shows prescription rates at VA hospitals across the country. But much like the disability claims backlog, the VA has taken steps to address the overprescription problem since our investigation broke. In February, senior VA officials told House lawmakers that the agency had reduced the number of veterans receiving opiates by more than 20,000 since October. Data obtained by CIR shows the number of veterans on opiates has continued to decline and is now 37,000 fewer than it was when our original story ran.

3. Failures in preventing veteran deaths back home

Though news of the 40 veterans who died while waiting for an appointment at the Phoenix VA sparked national outrage, preventable deaths have long been an issue at the agency. As CIR revealed in April, the VA paid out more than $200 million to nearly 1,000 families in wrongful death cases between 2001 and 2012. In May 2011, the 9th Circuit Court of Appeals in San Francisco accused the agency of “unchecked incompetence” and ordered it to overhaul the way it provides mental health care and disability benefits. And a 2012 inspector general review of a Bay Area veteran’s suicide revealed faulty communication inside the VA system that led to missed opportunities for help. With dozens of VA hospitals under investigation for abuses in scheduling practices, the agency has plenty of work ahead to ensure that veterans are receiving timely and proper care before it’s too late.

4. Major challenges for female veterans

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In 2012, photojournalist and filmmaker Mimi Chakarova’s documentary, “Her War,” highlighted the more than 3,000 female veterans living on U.S. streets. Many of these women had been sexually assaulted during their service (the Pentagon acknowledged this month a 50 percent surge in sexual assault reports last year), and they have different medical and psychological needs than male veterans. As News21 reported last year, the surge in female veterans returning from Iraq and Afghanistan presents the agency with ongoing challenges for adequate care.

5. Slow rollout of veteran health care centers at colleges

With hundreds of thousands of veterans using the GI Bill to go to college, health centers such as the one that opened at City College of San Francisco in 2010 were touted as a model for what the agency planned to expand at campuses across the country. But despite a $2.8 million annual budget, the VA’s initiative remains in a pilot stage.

6. Punishment of whistleblowers

Many of the VA problems highlighted by media in recent weeks were revealed by employees who stepped forward. But often, these workers have been reprimanded for speaking out against abuses within the agency. As CIR and ABC News revealed this month, a doctor at the VA hospital in St. Louis said he was removed from his position as chief of psychiatry after complaining of shoddy care. And in February, CIR and ABC also profiled a former VA doctor who says she was forced out after trying to limit the amount of opiate prescriptions given to patients. This blaming-the-messenger approach is not a new problem at the agency. On the VA benefits side, CIR reported in 2012 that an employee at the Oakland, California, VA lost her job after trying to help a veteran get disability compensation after he was wrongfully denied. Yet as The Atlantic’s Alesh Houdek writes, a major part of fixing the VA’s raft of problems lies in allowing employees to reveal wrongdoing without fear of retribution.

CIR will continue to investigate how U.S. veterans are treated and cared for after they return home, so sign up for our newsletter to get our latest coverage straight to your inbox.

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Cole Goins is the director of community engagement for Reveal, where he cultivates partnerships that blend in-depth journalism and creative public engagement. He has built and supported distribution networks, spearheaded arts-based initiatives such as the Off/Page Project, led social media and audience strategy, and facilitated statewide media collaborations. He was a senior fellow in the 2015 USC Annenberg Health Journalism Fellowships, mentoring five journalists on approaches to community engagement. Previously, Goins was the engagement editor at the Center for Public Integrity, where he led audience development initiatives and multimedia features for award-winning investigative projects. He earned a degree in journalism from the University of North Carolina at Chapel Hill, where he worked as music director for WXYC, the student-run radio station. He is based in Reveal's Emeryville, California, office.