Looking back, Mr. Trump’s response to the lawsuit can be seen as presaging his handling of subsequent challenges, in business and in politics. Rather than quietly trying to settle — as another New York developer had done a couple of years earlier — he turned the lawsuit into a protracted battle, complete with angry denials, character assassination, charges that the government was trying to force him to rent to “welfare recipients” and a $100 million countersuit accusing the Justice Department of defamation.

When it was over, Mr. Trump declared victory, emphasizing that the consent decree he ultimately signed did not include an admission of guilt.

But an investigation by The New York Times — drawing on decades-old files from the New York City Commission on Human Rights, internal Justice Department records, court documents and interviews with tenants, civil rights activists and prosecutors — uncovered a long history of racial bias at his family’s properties, in New York and beyond.

That history has taken on fresh relevance with Mr. Trump arguing that black voters should support him over Hillary Clinton, whom he has called a bigot.

While there is no evidence that Mr. Trump personally set the rental policies at his father’s properties, he was on hand while they were in place, working out of a cubicle in Trump Management’s Brooklyn offices as early as the summer of 1968.

Then and now, Mr. Trump has steadfastly denied any awareness of any discrimination at Trump properties. While Mr. Trump declined to be interviewed for this article, his general counsel, Alan Garten, said in a statement that there was “no merit to the allegations.” And there has been no suggestion of racial bias toward prospective residents in the luxury housing that Mr. Trump focused on as his career took off in Manhattan in the 1980s.

In the past, Mr. Trump has treated the case as a footnote in the narrative of his career. In his memoir “The Art of the Deal,” he dispensed with it in five paragraphs. And while stumping in Ohio, he even singled out his work at one of his father’s properties in Cincinnati, omitting that, at the time, the development was the subject of a separate discrimination lawsuit — one that included claims of racial slurs uttered by a manager whom Mr. Trump had personally praised.