See pages 249-251 of Garey and Johnson, Computers and Intractability, for a dozen NP-complete problems in Number Theory.
EDIT: A couple of examples, by request.
AN2, Simultaneous incongruences. Given a collection $\lbrace(a_1,b_1),\dots,(a_n,b_n)\rbrace$ of ordered pairs of positive integers with $a_i\le b_i$ for $1\le i\le n$, is there an integer $x$ such that for all $i$, $x\not\equiv a_i\pmod{b_i}$?
AN4, Comparative divisibility. Given sequences $a_1,a_2,\dots,a_n$ and $b_1,b_2,\dots,b_m$ of positive integers, is there a positive integer $c$ such that the number of $i$ for which $c$ divides $a_i$ is more than the number
of $j$ for which $c$ divides $b_j$?