Prion diseases are diseases of protein conformation. Structure‐dependent antibodies have been sought to probe conformations of the prion protein (PrP) resulting from environmental changes, such as differences in pH. Despite the absence of such antibodies for full‐length PrP, a recombinant Fab (D13) and a Fab derived from mAb 3F4 showed pH‐dependent reactivity toward epitopes within the N‐terminus of N‐terminally truncated PrP(90–231). Refolding and maintaining this protein at pH ≥5.2 before immobilization on an ELISA plate inhibited reactivity relative to protein exposed to pH ≤4.7. The reactivity was not affected by pH changes after immobilization, showing retention of conformation after binding to the plate surface, although guanidine hydrochloride at 1.5–2 M was able to expose the cryptic epitopes after immobilization at pH ≥5.2. The α‐helical CD spectrum of PrP(90–231) refolded at pH 5.5 was reduced somewhat by these pH changes, with a minor shift toward β‐sheet at pH 4 and then toward coil at pH 2. No covalent changes were caused by the pH differences. This pH dependence suggests titration of an acidic region that might inhibit the N‐terminal epitopes. A similar pH dependence for a monoclonal antibody reactive to the central region identified an acidic region incorporating Glu152 as a significant participant. Proteins 2001;44:110–118. © 2001 Wiley‐Liss, Inc.