Use \Big or \bigg; my preference would go to the former. It's not necessary that the parentheses encompass the whole contents, they are just delimiters. Surely having them asymmetric with respect to the formula axis would be worse.
\documentclass{article}
\usepackage{amsmath,amssymb}
\begin{document}
\[
\varphi^{-1}\left(\bigcap_{\substack{\mathfrak{p} < B \\ p \text{ prime}}} \mathfrak{p}\right)
\]
\[
\varphi^{-1}\Bigl(\bigcap_{\substack{\mathfrak{p} < B \\ p \text{ prime}}} \mathfrak{p}\Bigr)
\]
\[
\varphi^{-1}\biggl(\bigcap_{\substack{\mathfrak{p} < B \\ p \text{ prime}}} \mathfrak{p}\biggr)
\]
\end{document}

Compare with
\[
\varphi^{-1}
\mathopen{\raisebox{-1.8ex}{$\Biggl($}}\,
\bigcap_{\substack{\mathfrak{p} < B \\ p \text{ prime}}} \mathfrak{p}
\mathclose{\raisebox{-1.8ex}{$\Biggr)$}}
\]
where the parentheses have been shifted down

\bigcapwill not be vertically centred on the math axis. Alternatively, shrinking the brackets without raising the internal content would make this look too low. – Werner Apr 14 '13 at 05:55_p_ primeto the end of the equation? Something like.../right) \quad\forall\quad p\in\mathcal{P}where\mathcal{P}is the set of prime numbers of interest? – Holene Apr 14 '13 at 06:44