Aleinu is a relatively short prayer that marks the end of all three daily prayer services. Its two paragraphs express both particularistic and universalistic themes: The first paragraph speaks of a specifically Jewish obligation to praise God ("It is our duty to praise the Master of all..."). The second paragraph calls for universal recognition of God by all people ("and all humanity will call upon your name"). It closes by invoking collective recognition of God, citing the verse "And the Lord shall be king over all the earth; in that day there shall be one Lord with one name" (Zechariah 14:9).
Commenting on Aleinu's prominence in Jewish prayer services, Ismar Elbogen, a 20th-century scholar of Jewish liturgy, said it was certainly significant that "the idea of... the future union of all mankind... in the service of the one God became part of the daily service."
Both paragraphs of Aleinu are recited in a standing position. During the first paragraph, it is customary to bow while saying the words, "We bend the knee and bow."
Though the second paragraph of Aleinu expresses a harmonious vision of collective recognition of God, Aleinu has caused a fair bit of discord at various points in history. Particularly contentious is the line in Aleinu's first paragraph, praising God: "who has not made us like the nations of the world and has not placed us like the families of the earth; who has not designed our destiny to be like theirs, nor our lot like that of all their multitude, for they bow to vanity and emptiness and pray to a god who cannot save."
When reciting the end of this line, Jews used to spit, because "emptiness" and "spit" share the same Hebrew consonants (r-i-k). Some synagogues were even constructed with special spittoons in their pews, designated for this part of the service.
Not surprisingly, Christians of the Middle Ages were angered by this line, assuming the "god who cannot save" referred to Jesus. Church decrees, government edicts, and censors sometimes demanded Jews omit this reference--even as late as 1750 in Prussia. In other cases, Jews took it upon themselves to omit this line, probably out of fear that including it would incite further Christian persecution.
As the line fell out of use, so did the custom of spitting. Today, many Jews, including some Orthodox Jews, still omit the reference (and the spit).
Yet Jewish tradition does not associate the "god who cannot save" with Jesus specifically. The Prophet Joshua is traditionally considered the author of Aleinu (Teshuvot ha-geonim, Gates of Repentance, #43). He was thought to have composed the prayer when he was about to conquer the city of Jericho--long before Jesus' lifetime.
Most scholars, however, credit Rav, a third century Babylonian sage, with writing Aleinu. Certain phrases which occur in the prayer, such as "the supreme Sovereign of sovereigns" and "the Holy One, blessed be" are rabbinic phrases, and would not have been used by Joshua.
Scholars also cite the original context of Aleinu as evidence for Rav's authorship of the prayer. Aleinu got its start in Jewish liturgy as the opening of the malkhuyot section of the Rosh Hashanah musaf liturgy, in which Jews declare God to be their Sovereign. This entire section of liturgy is attributed to Rav, including Aleinu. In his ancient Babylonian context, it is more likely Rav had pagans, not Christians, in mind, when writing about those who worship a "god who cannot save."
Israel Ta-Shma, a scholar of Jewish history who taught at Hebrew University in the 20th century, noted a French version of Aleinu, preserved in a 12th-century English manuscript. In this version of Aleinu the passage which so angered Christians reads: "for they bow to vanity and emptiness and pray to a god who cannot save: a man, dust, blood, bile, dangling flesh, a worm, impure ones, adulterers…"
It seems from this text that some Jews in medieval France modified the text of Aleinu to reflect their experiences. They added to a line which previously had not referred to Christians, so that it would become an anti-Christian polemic. This version of Aleinu is the exception that proves the rule: the text of Aleinu did not (and does not) refer to Christians.
Modern Jews have also tackled the difficult language of Aleinu. Early Reform prayer books in Europe and America omitted the prayer entirely. Both the 20th-century Reform Gates of Prayer (1975) and the recently published Mishkan Tefillah offer several different versions of Aleinu, one of which includes the traditional Hebrew text (without the reference to "a god who cannot save."). The English is translated euphemistically to avoid potentially offensive ideology being expressed by the worshipper. A similar approach is taken by the Conservative Siddur Sim Shalom which translates: "He [God] made our lot unlike that of other people, assigning to us a unique destiny"—a euphemistic translation of the original Hebrew. No Reform, Conservative or Reconstructionist prayer books retain the reference to "a god who cannot save."
Despite the strong Christian reaction to the harsh language of the prayer's opening paragraph, Aleinu grew in popularity among medieval Jews.
In The Vale of Tears, a 16th-century martyrology (a catalogue of martyrs), Joseph Ha-Kohen describes the persecution of the Jews of Blois, France in 1171:
Many Masters of the Torah died at the stake [and] the death of the saints was accompanied by a solemn song resounding through the stillness of the night, causing the Churchmen who heard it from afar to wonder at the melodious strains, the like of which they had never heard before. It was ascertained afterwards that the martyred saints had made use of the Aleinu as their dying song.
We do not know whether these martyrs sang Aleinu because they identified their persecutors with the negative description of gentiles in the first paragraph of the prayer, or because they wanted to stress their hope of universal recognition of God which would include their persecutors. But this story does illustrate that Aleinu was an important and well-known prayer, as early as the 12th century.
Over time, Jews began to recite Aleinu at the end of the morning and evening services, probably because Aleinu's theme of universal recognition of monotheism complemented the Shema, which was said during morning and evening services. And eventually Aleinu was included in afternoon services too--another testament to its growing popularity.
Siddur: Prayer Book Articles