Junior doctors have lost their High Court battle to invalidate their NHS job application process.
MTAS has been widely criticised by doctors
Pressure group Remedy UK had challenged the legitimacy of a new computerised application system, calling for medics to be re-interviewed for posts.
The government had already agreed the forthcoming second round of interviews should use the old CV-based system.
The judge ruled against invalidating the interviews already done but said medics were justified to feel angry.
Mr Justice Goldring said the premature introduction of the new system has had disastrous consequences - and although the legal challenge has failed many junior doctors have "an entirely justifiable sense of grievance".
He added individual medics might still have good grounds for appeal under employment law.
The British Medical Association had not supported the Remedy UK challenge.
While it had been highly critical of the new system, it said invalidating the first round of interviews would just "prolong the agony".
The Medical Training Application Service (MTAS) has been dogged by controversy in recent months.
The system was introduced as part of the Modernising Medical Careers initiative aimed at cutting the number of years of training needed for doctors to reach consultant level.
MTAS was designed to speed up the selection process, but doctors said the forms were badly worded, did not ask pertinent questions or allow them to set out relevant qualifications and experience, and had no facility for attaching a CV.
This resulted in many doctors not being selected for their first-choice NHS trusts, and a significant number not getting any interviews at all.
Junior doctors applying to start their specialist training this year are having to compete for a limited number of training places with those who are part-way through their training under the old system under the Modernising Medical Careers initiative.
It means over 30,000 doctors are chasing about 20,000 specialist training places. There will still be thousands of NHS jobs available, but these will not count towards their training to becoming a GP or senior doctor.
Ministers have already announced that after the first recruitment round, MTAS will not be used again this year, leaving follow-up recruitment rounds probably involving about 7,000 posts dependent on more traditional CVs.
Remedy UK was originally arguing for the system to be scrapped, and all the interviews carried out again.
But it then called for the appointments which are due in a couple of weeks from the first round of interviews to be made on a temporary basis - as there would not be enough time to complete its preferred process by 1 August when the doctors have to be in place.
It had argued that the whole appointment process could then be redone in six or 12 months' time.
A spokesman for Remedy UK called it a "sad day" for junior doctors, but said the group would not be appealing the decision.
"We are bitterly disappointed. The judgment accepts that the careers and lives of thousands of talented doctors in this country may be harmed."
Health Minister Lord Hunt said the government would now be working to establish the best possible way forward to match doctors to posts.
"We understand the uncertainty that problems with the system has caused junior doctors and their families, and acknowledge the criticisms that the judgement contains."
Dr Jo Hilborne, chairman of the BMA junior doctors committee, said the handling of the whole situation was a "mess" and "the careers of thousands of doctors remain in doubt because of government failures".