The case of Kotteakos et al. v. United States involves the conviction of the petitioners for conspiring to violate the National Housing Act. The question is whether the petitioners were substantially prejudiced by being convicted of a single general conspiracy when the evidence proved eight or more different ones executed through a common key figure. The government's evidence was not contested by the petitioners, apart from alleged errors relating to proof and instructions at the trial. The Court of Appeals found that the trial judge was wrong in assuming there was only one conspiracy and should have dismissed the indictment. However, the appellate court held that the error was not prejudicial and it was proper to join the conspiracies. The government admits there was a variance in proof from the single conspiracy charged in the indictment, but argues that it was not prejudicial to the petitioners.

Berger v. United States ruled that a variance in proof from one conspiracy charged to two conspiracies proved was not fatal if it did not affect the substantial rights of the accused. However, this case cannot be used as a precedent in this case because the trial court's instruction that there was only one conspiracy was plainly wrong and had far-reaching effects. The government's argument that the variance error is harmless if the evidence offered to convict each defendant would be sufficient in a separate trial is not the test under § 269. The trial judge's misunderstanding that there was only one conspiracy affected the proof of overt acts.

The court found errors in the trial judge's instructions and emphasized the importance of individualizing each defendant's role in the conspiracy. The Supreme Court found that the right not to be tried en masse for distinct and separate offenses committed by others was violated. The government consolidated eight separate crimes for trial when the only connection between them was one person's participation, which violated proper joinder. The error in the charge as to the conspiracy did not substantially injure the defendants. The objection that the several conspiracies were not joined as separate counts in one indictment is purely formal, as they were acts or transactions of the same class of crimes or offenses, and there is no evidence of prejudice.