The most significant short-term effect of the decision made in Marbury v. Madison was the fact that it greatly magnified the court's authority and opinion, though it can be debated that this is also a long-term effect. Another short-term effect is the fact that the decision was a major slap at the Jeffersonians, who were very thirsty to prevent such a thing and to remove any traces of a Federalist influence in court, despite the fact that Jefferson flip-flopped on his political views several times later on. As a result of that, the Jeffersonians attempted to impeach Samuel Chase, a Federalist judge serving on the Supreme Court, because he spoke out against the Republicans. Though he was found not guilty of the charges brought against him (high crimes and misdemeanors), he became deeply unpopular and scorned by the public. The short-term effects of the decision in Madison v. Marbury were certainly important, the long-term effects certainly outweigh them.
Another significant effect of the decision in the Marbury v. Madison case was the decision that confirmed the legality of the Louisiana Purchase of America from France in 1803. The Louisiana Purchase was the act that doubled the size of the