Shares of large banking companies have taken a beating in the last three months, but a rally of sorts has lifted those of smaller ones high enough to trigger worries that prices will outpace returns.

For the most part, these smaller companies have avoided the credit quality issues and slowdown in profit growth that have plagued the larger banks. Their share prices have risen as investors have fled risk in search of value. But the rise may have reached a limit. On Wednesday, Jeffrey A. Miller, an analyst and portfolio manager at Acadia Research Group in West Conshohocken, Pa., downgraded five of the 13 banks he covers because they have hit his price targets.

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