Harvard Management Company (HMC), investment manager of the largest U.S. university endowment plan, has been one of the more active users of ETFs among university endowments.

The investment firm's use of ETFs dates back at least several years and HMC is also known for embracing an array of emerging markets funds.

Something else that drew little attention was the degree to which HMC slashed its exposure to emerging markets ETFs in the fourth quarter.

From Chile to China to India, HMC pared stakes in plenty of popular, country-specific emerging markets ETFs during the last three months of 2012.

The iShares MSCI Chile Capped Investable Market Index Fund (ECH) was just one of the emerging markets ETFs where HMC has reduced its exposure. HMC held nearly 439,250 shares of the lone Chilean ETF at the end of the fourth quarter, a 13% reduction from the prior three-month period.

Elsewhere in Latin America, HMC reduced its exposure to the iShares MSCI Mexico Capped Investable Market Index Fund (EWW) by 25%, to about 384,470 shares. HMC also reduced its stake in EWW's largest holding, mobile phone carrier America Movil (AMX), by three percent while leaving unchanged its position in EWW's second-largest holding, Fomento Economico (FMX).

The endowment plan manager also lowered its stake in the iShares MSCI Brazil Capped 

Index Fund (EWZ) by eight percent last quarter. HMC's positions in Petrobras (PBR) and Vale (VALE), EWZ's two largest holdings, were unchanged. HMC also liquidated its entire stake in the iShares S&P Latin America 40 Index Fund (ILF).

Perhaps in a sign that some professionals are starting to realize there are better ways to grab ETF exposure to China, HMC slashed its investment in the iShares FTSE China 25 Index Fund (FXI) by 44%  in the fourth quarter.

That may sound like a lot, but HMC also liquidated all of its positions in the WisdomTree India Earnings ETF (EPI) and the iShares MSCI Poland Capped Investable Market Index Fund (EPOL).

HMC's stakes in some of FXI's top-10 holdings, including China Mobile (CHL) and CNOOC (CEO), were unchanged.

Staying in Asia, HMC lowered its stake in the iShares MSCI South Korea Index Fund (EWY) by 18%, but left unchanged its investments in the iShares MSCI Malaysia Index Fund (EWM) and the iShares MSCI Philippines Investable Market Index Fund (EPHE). HMC also did not alter its position in the Market Vectors Indonesia ETF (IDX), the management firm's fifth-largest holding.

HMC also cut its investment in the iPath MSCI India Index ETN (INP) by 48 percent to just over 401,200 shares. The firm also sold nearly 2,300 shares of the iShares MSCI Turkey Investable Market Index Fund (TUR) in the quarter.

However, while HMC was busy reducing exposure to emerging markets ETFs, it did add to some of its U.S.-focused positions. HMC's investments in the iShares Core S&P 500 ETF (IVV) and the iShares Russell 2000 Index Fund (IWM) grew by four and six percent, respectively, during the fourth quarter. HMC also added seven percent to its stake in the Vanguard Dividend Appreciation ETF (VIG), the largest dividend ETF by assets.

During the fourth quarter, HMC slashed its stake in the iShares MSCI EAFE Index Fund (EFA) by 80%, reducing its investment in that ETF by over 126,300 shares to just under 30,000 shares, according to the most recent 13F. The firm also added a new investment in the Vanguard MSCI EAFE ETF (VEA) of almost 232,400 shares.

HMC was also active with commodities funds during the fourth quarter, reducing positions in the PowerShares DB Agriculture Fund (DBA) and the PowerShares DB Energy Fund (DBE). The firm added to positions in the PowerShares DB Base Metals Fund (DBB) and the PowerShares DB Precious Metals Fund (DBP).

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