AN ASTONISHING 98.6 percent of those eligible turned out to vote Monday in East Timor in a referendum on independence from Indonesia. People risked attack and braved intimidation to register their views. One 23-year-old man, who had been wounded by anti-independence militia, arrived on a stretcher with an intravenous drip. "I want freedom," Usulau de Jesus Cepeda told a reporter from the New York Times. "It's now or never."

The militias who assaulted Mr. Cepeda remain the dangerous wild card for East Timor, a former Portuguese colony that was brutally recolonized by Indonesia two decades ago and has strived for independence ever since. The results of Monday's U.N.-supervised referendum won't be known for a week, but the turnout points to a substantial pro-independence majority. How will the militias -- which have been armed and encouraged by Indonesia's armed forces -- respond?

The answer lies to a large extent with Indonesia, which can control the militias if it chooses. But Indonesia is also in transition; the Suharto dictatorship fell more than a year ago; and what will take its place is not yet entirely clear. President B. J. Habibie, who may be a transitional leader, agreed to hold a referendum, recognizing that Indonesia was being harmed by the repressive tactics needed to hold East Timor against its will and by the resulting bad publicity abroad. But elements of the government and military may not have made their peace with his decision.

President Clinton wrote to Mr. Habibie in advance of the election reminding him of how important the United States considered a free and fair vote. The election did proceed more smoothly than many had feared, though one U.N. staffer was murdered. The day after the election, however, was far less peaceful, with the militias once again blustering and attacking. Mr. Clinton and Indonesia's other friends overseas may once again be called on to communicate to Mr. Habibie how much is at stake, for Indonesia as well as for East Timor.