IF YOU IMAGINE the nation’s prosecutors regularly going to trial to convict the bad guys, imagine again.

The Wall Street Journal reported recently that 97 percent of cases the Justice Department prosecuted last year ended with guilty pleas, up from 84 percent in 1990. The ratio is nearly as high at the state level. “Criminal justice today is for the most part a system of pleas, not a system of trials,” Justice Anthony M. Kennedy wrote this year.

In plea bargains, defendants can minimize the risks they face, and prosecutors can save time, effort and money. This keeps the courts from becoming totally overloaded. Yet there’s a risk that those who have reasonable claims to innocence will be unreasonably discouraged from pressing for a trial. Those who do opt to plea-bargain should be able to expect a fair process.

The Journal’s story about Kenneth Kassab, who pulled out of a plea deal at the last minute and was eventually acquitted, points to plea bargaining’s possible deficiencies. When sentencing authority is effectively moved from judges to prosecutors, not all the protections defendants would receive at trial come along. Most obviously: the requirement to hear complete accounts of both sides’ case and all mitigating circumstances.

Prosecutors can load up on charges they can later drop, pressuring defendants to cooperate before trial and plead guilty. Prosecutors’ need for information may end up benefiting more serious criminals, while judges might be more tempted to show leniency to low-level players.

According to an analysis last year from the Justice Department’s Bureau of Justice Assistance, some research on state-level sentencing also suggests that the exercise of prosecutorial discretion in plea bargaining can result in disparate outcomes of a more troubling nature — across different regions and across different types of defendants, with black defendants less likely than white ones to obtain a reduced charge.

On its own, the high number of guilty pleas is not proof of a problem that demands an aggressive response across the federal and various state systems. The Justice Department already expects prosecutors to ensure that plea deals are fair. Federal judges have discretion to review deals. Public defenders on the federal level are generally excellent, which probably make things fairer than in some states.

But, recognizing the primary role that plea bargaining has come to play in the justice system, the Supreme Court this year began to extend judicial supervision over the process, ruling that defendants have a right to competent counsel in plea negotiations. The justices should not be the only ones examining the dominance of plea bargaining. State officials, legal scholars, the Justice Department and perhaps Congress should more thoroughly consider whether and how to make the nation’s system of pleas, not of trials, more predictable or procedurally sound.