Shiller, who developed the CAPE ratio along with colleague John Campbell, said that the measure, which looks at P/E ratios averaged over the preceding 10 years, showed that stock prices have been relatively high over the past two decades.
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But those valuations could soon take a hit, he added.
"There's instability in the world economy," he said. "The Fed is tapering."
Bonds, too, were in a similar boat, Shiller said, citing Treasury Inflation-Protected Securities.
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"We've had negative TIP rates recently, so what's going on here? How can it be that 30-year TIPS were negative in 2012? How can it be that people think that we can get a return, a riskless return in real terms for 30 years? There's something bizarre," he said. "That looks a little like a bubble, as well. So, the whole thing might correct down, both bonds and stocks."
As if overvaluations in bonds and stocks weren't enough, Shiller also said that housing could be getting lofty.
"I've been kind of surprised by the housing market. It bottomed out in 2012. It's up something like 25 percent, in some cities much more than that," he said. "So, we are seeing a sort of boom in the housing market.
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"So, you know, we've got stocks and bonds highly priced, and now we're starting to see housing maybe going in the same direction. It's like everything, everything is pricey."
The reason, Shiller added, could be a counterintuitive one.
"It might seem perverse, but worries about the future can actually cause asset markets to be priced highly," he said. "I called it the life-preservers-on-the-Titanic theory. When the Titanic was going down, people would pay a fortune for anything that floats. … I'm exaggerating, of course, but that might be the situation we're in now."
—By CNBC's Bruno J. Navarro.