Experts from Berlin's Robert Koch Institute said a 22-year-old woman in Hamburg and a 37-year-old woman in Kulmbach, Bavaria were both infected with the virus. The Bavarian Health Ministry reported a man in Regensburg also had swine flu early in the morning.
All three recently returned from trips in Mexico.
There are several other cases being investigated and health officials plan to meet a plane from Cancun in Munich on Wednesday to examine the passengers.
Other people are under observation in Hamburg and the state of North Rhine-Westphalia.
On Tuesday German Health Minister Ulla Schmidt said Germany was prepared to handle a pandemic if the swine flu situation escalates.