The third quarter saw a strong comeback period for open-ended mutual funds, and a stellar one for exchange-traded funds, according to Morningstar.

Mutual funds’ net inflows totaled $144.7 billion. That’s a stark reversal from the third quarter of 2008, when investors pulled $70.4 billion out of mutual funds followed up in the fourth quarter by outflows of $180.5. Exchange-traded funds took in $22 billion, helping to push total ETF assets over the $700 billion mark.

The third quarter results brought the year-to-date total for mutual-fund net inflows to $273.2 billion.

Bond funds captured the vast majority of inflows in the third quarter, reaping $120 billion for the period. But Morningstar says that bond funds might be in for a change of course after a quarter of double-digit investment returns. “Bond funds have had a nice run and it wouldn’t be surprising if they were in for a breather,” said Sonya Morris, Morningstar’s editorial director of mutual fund research.

U.S. stock funds did not share in the bounty. So far this year, investors have put just $3.8 billion back into U.S. stock funds, Morningstar said. 

ETFs are continuing to skyrocket. Investors poured $5.4 billion into U.S.-traded ETFs in September alone, helping to push the year-to-date total new inflows to about $56.3 billion. ETF industry flows have been very strong so far in 2009, with positive flows in every month except February, when investors pulled out roughly $5.5 billion.

Taxable-bond ETFs attracted the most net new assets in September, about $3.2 billion, compared with $2.8 billion for international stock ETFs, $1.8 billion for alternatives, $1.4 billion for commodities, $329 million for municipal bonds and $59 million for balanced.

Tepid investor interest in U.S. stocks continued, with $4.3 billion in net redemptions for the month.

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