National Crime Agency (NCA) investigators along with officers from West Yorkshire Police, arrested Yusuf Kara, 30, of Lidget Green, Bradford, and Imran Khan Ashraf, 31, of no fixed address but formerly of Bradford, on Thursday in connection with the distribution of heroin in the Yorkshire and Humber region.
Kara and Ashraf appeared at Leeds Crown Court on Saturday, charged with conspiracy to supply class A drugs and money laundering.
They were remanded in custody and will next appear at Leeds Crown Court on November 18.
The NCA said Ashraf was arrested after officers who stopped him as he drove his van in Bolton found approximately £100,000 in cash hidden under a false floor in the vehicle.
Kara was later arrested on Shearbridge Road, Bradford. Officers then searched his house and found 56 packages, each containing 1kg of heroin, with a street value of between £2.5 and £3 million, hidden in bags and a suitcase, according to the NCA.
NCA operations manager Brent Lyon said: "The seizure of this significant amount of heroin is a big step towards protecting the public from the damage and devastation drugs cause."