A trader borrows 5000 from a financial institution at 4% rate of interest per annum. He repays 1000 at the end of each year. How much does he still have to pay after the third year?

At the end of the first year, the trader still has to pay 5000 - 1000 = <<5000-1000=4000>>4000 dollars

At the end of the second year, the trader still has to pay 4000 - 1000 = <<4000-1000=3000>>3000 dollars.
At the end of the third year, the trader still has to pay 3000 - 1000 = <<3000-1000=2000>>2000 dollars. Answer: \boxed{2000}.