Jane died in Manchester of bubonic plague and was buried in the Manchester Cathedral burial grounds in March 1604. Michael, born in Prague, died on his father's birthday in 1594. Theodore, born in Třeboň, died in Manchester in 1601. His sons Arthur Dee and Rowland survived him, as did his daughter Katherine, "his companion to the end". No records exist for his youngest daughters Madinia (sometimes Madima), Frances and Margaret after 1604, so it is widely assumed they died in the epidemic that took their mother. (Dee had by this time ceased to keep a diary.)