Four people died and 102 were injured when the King's Cross to Leeds train came off the tracks at 115mph on October 17, 2000.
The prosecution alleged the derailment occurred because of a cavalier approach to safety.
The defence argued it was unfair to make the five rail executives scapegoats.
They worked in an under-funded industry which had been neglected by governments for more than 40 years, Jonathan Goldberg QC, defending one of the men, told the court.
The five men had originally faced manslaughter charges - together with the engineering giant Balfour Beatty, the company responsible for track maintenance.
But these were thrown out by the judge, Mr Justice Mackay half way through the trial after legal submissions from the defence.
The decision again highlighted the difficulty of securing convictions of companies for corporate manslaughter under the current legislation.
Long-awaited reform of the law is proposed by the Government but is still at draft stages.
After the company was cleared of corporate manslaughter, Balfour Beatty admitted it had breached safety standards.
But it did not accept all that was alleged against it.
The trial of the five "human" defendants together with Network Rail continued - with all denying any breach of safety laws.
The individual defendants charged were Balfour Beatty Rail Maintenance Limited's regional director Anthony Walker, 48, Nicholas Jeffries, 50, civil engineer for the same firm, Railtrack North Eastern managers Alistair Cook, 52, and Sean Fugill, 52, and Railtrack LNE track engineer Keith Lea, 55.
The men shook hands with each other and their counsel after they were cleared today at the end of a seven month trial.
Network Rail and Balfour Beatty will be be sentenced on October 3 for the health and safety offences.
The jury of 10 men and one woman had spent 15 hours over four days considering their verdicts.
They had heard the prosecution allege a catalogue of safety lapses in the run-up to the fatal derailment.
* A faulty rail at the crash site which was identified 21 months before the crash but left unrepaired - although a replacement rail had been delivered and left alongside it for six months.
* Speed restrictions were not imposed in the area of that faulty rail.
* A backlog of essential work had been allowed to accumulate which could have closed down King's Cross station if the rule book had been followed.
* The clock which counted the time for carrying out all of the out-of-date repairs was turned back to zero on the backlog of 200 defects in the first 43 miles of the track from King's Cross.
Prosecutor Richard Lissack said that "this cavalier approach to the safety of those in trains" was finally realised on October 17, 2000.
But their lawyers argued they were not to blame.
Mr Goldberg, defending Jeffries, told the jury: "They were all honourable men doing their duty.
"These five men worked in an under-funded, under-invested railway industry, which had been neglected by governments of all parties for over 40 years and which had recently undergone a botched and unworkable privatisation," maintained Mr Goldberg.
"They inherited this awful system and they tried to make it work for the benefit of the travelling public but they did not invent it.
"It is a sad reflection on political correctness and the blame culture of modern- day Britain that five men at modest job levels are blamed for Hatfield whilst the concerned and grieving relatives and the Press and public are fed the line that the buck stops with them."
Railtrack had denied breaching its health and safety duty.
Nigel Sweeney QC, representing the company, said it had warned contractors Balfour Beatty that checks on problem lines should be stepped up before the crash.
He said that Railtrack had no obligations to double-scrutinise in detail the maintenance carried out by an independent contractor.
The company had taken reasonable steps to manage the problems it faced, he argued.
The Hatfield crash victims were Steve Arthur, 46, from Pease Pottage, West Sussex; Peter Monkhouse, 50, of Headingley, Leeds; Leslie Gray, 43, of Tuxford, Nottingham; and Robert James Alcorn, 37, of Auckland, New Zealand.