The HRV contains thousands of footnotes. In the Tanak portion these footnotes indicate alternate readings from various witnesses including the alternate readings given in the Masorah (marginal notes to the Masoretic Text) such as the 134 places where the Masorah indicates the scribes had revised YHWH to ADONAI.

In the NT portion the HRV footnotes indicate places where the NT has quoted or cited the Tanak, alternate readings from various versions including marginal notes to some Greek manuscripts referring to alternate readings found in the Judaikon (Jewish Version).

These footnotes also indicate places where the Greek translator appears to have misunderstood an ambiguous Hebrew/Aramaic word, or misread a word as another word of similar appearance, and wordplays in the Hebrew or Aramaic.