The Church of England's governing body is meeting in York, amid tension over the short-lived appointment of a homosexual priest as Bishop of Reading.
Dr Williams addresses the synod on Monday
The business committee of the general synod has been meeting to decide whether to hold an emergency debate on Canon Jeffrey John's sudden resignation.
Whether or not there is a formal debate on the issue, commentators say it seems set to overshadow all other items on the agenda.
These include relations between the Anglican and Methodist Churches, racial justice and embryo research.
Dr John, who will not attend, is believed to have timed last week's resignation to avoid a crisis at the synod.
But BBC religious affairs correspondent Robert Pigott says the affair has left liberal and traditionalist members of the synod more divided than at any time since the dispute over the ordination of women a decade ago.
And Archbishop of Canterbury Rowan Williams is expected to refer to it in his first presidential address on Monday morning.
Canon Jeffrey John decided not to take up the post of bishop
Dr John, who was due to be consecrated on 9 October, has been in a relationship with a man for 27 years, but says he is now celibate.
The decision to make him the Bishop of Reading prompted a crisis within the church, with nine senior bishops writing to national newspapers to express their anger.
The Archbishop of Nigeria, the leader of the world's biggest Anglican community, threatened to break ties with the Church if the appointment went ahead.
The other big issue before the synod's five-day meeting is the Anglican-Methodist covenant - an agreement for the two Churches to work together.
The Methodist Church approved the covenant by 277 votes to 86 at their conference in Llandudno, Conwy, last week, and the synod is expected to follow suit.
In a debate on racial justice, the synod will set out the Anglican response to the Stephen Lawrence inquiry and give details of ethnic minority participation at all levels of the Church.