Hostilities broke out on the night of February 4, 1899, after two American privates on patrol killed three Filipino soldiers in a suburb of Manila. Thus began a war that would last for more than two years. Some 126,000 American soldiers would be committed to the conflict 4,234 American and 16,000 Filipino soldiers, part of a nationwide guerrilla movement of indeterminate numbers, died.

The Filipino troops, armed with old rifles and bolos and carrying anting-anting (magical charms), were no match for American troops in open combat, but they were formidable opponents in guerrilla warfare. For General Ewell S. Otis, commander of the United States forces, who had been appointed military governor of the Philippines, the conflict began auspiciously with the expulsion of the rebels from Manila and its suburbs by late February and the capture of Malolos, the revolutionary capital, on March 31, 1899. Aguinaldo and his government escaped, however, establishing a new capital at San Isidro in Nueva Ecija Province. The Filipino cause suffered a number of reverses. The attempts of Mabini and his successor as president of Aguinaldo's cabinet, Pedro Paterno, to negotiate an armistice in May 1899 ended in failure because Otis insisted on unconditional surrender.

Still more serious was the murder of Luna, Aguinaldo's most capable military commander, in June. Hot-tempered and cruel, Luna collected a large number of enemies among his associates, and, according to rumor, his death was ordered by Aguinaldo. With his best commander dead and his troops suffering continued defeats as American forces pushed into northern Luzon, Aguinaldo dissolved the regular army in November 1899 and ordered the establishment of decentralized guerrilla commands in each of several military zones. More than ever, American soldiers knew the miseries of fighting an enemy that was able to move at will within the civilian population in the villages. The general population, caught between Americans and rebels, suffered horribly.

According to historian Gregorio Zaide, as many as 200,000 civilians died, largely because of famine and disease, by the end of the war. Atrocities were committed on both sides. Although Aguinaldo's government did not have effective authority over the whole archipelago and resistance was strongest and best organized in the Tagalog area of Central Luzon, the notion entertained by many Americans that independence was supported only by the "Tagalog tribe" was refuted by the fact that there was sustained fighting in the Visayan Islands and in Mindanao. Although the ports of Iloilo on Panay and Cebu on Cebu were captured in February 1899, and Tagbilaran, capital of Bohol, in March, guerrilla resistance continued in the mountainous interiors of these islands. Only on the sugar-growing island of Negros did the local authorities peacefully accept United States rule. On Mindanao the United States Army faced the determined opposition of Christian Filipinos loyal to the republic.

Aguinaldo was captured at Palanan on March 23, 1901, by a force of Philippine Scouts loyal to the United S8df States and was brought back to Manila. Convinced of the futility of further resistance, he swore allegiance to the United States and issued a proclamation calling on his compatriots to lay down their arms. Yet insurgent resistance continued in various parts of the Philippines until 1903.

The Moros on Mindanao and on the Sulu Archipelago, suspicious of both Christian Filipino insurrectionists and Americans, remained for the most part neutral. In August 1899, an agreement had been signed between General John C. Bates, representing the United States government, and the sultan of Sulu, Jamal-ul Kiram II, pledging a policy of noninterference on the part of the United States. In 1903, however, a Moro province was established by the American authorities, and a more forward policy was implemented: slavery was outlawed, schools that taught a non-Muslim curriculum were established, and local governments that challenged the authority of traditional community leaders were organized. A new legal system replaced the sharia, or Islamic law. United States rule, even more than that of the Spanish, was seen as a challenge to Islam. Armed resistance grew, and the Moro province remained under United States military rule until 1914, by which time the major Muslim groups had been subjugated (see Islam , ch. 2).

Data as of June 1991