The Queen spoke today of the "difficult" and even "painful" choices facing the Church of England as she formally opened the Church's national assembly.
The five years ahead will not always be "straightforward", she told lay members, clergy and bishops gathered at Church House in Westminster, central London.
"The new Synod will have many issues to resolve to ensure that the Church of England remains equipped for the effective pursuit of its mission and ministry," she said.
"Some will, no doubt, involve difficult, even painful, choices.
"But Christian history suggests that times of growth and spiritual vigour have often coincided with periods of challenge and testing.
"What matters is holding firmly to the need to communicate the gospel with joy and conviction in our society."
Her remarks are likely to be interpreted as referring to the new General Synod's central role in legislation to introduce women bishops.
The Church of England is also being asked to consider the Anglican Covenant, billed as a blueprint to help the Anglican Communion resolve disputes over homosexuality and same-sex blessings.
"For at the heart of our faith stand not a preoccupation with our welfare and comfort but the concepts of service and of sacrifice as shown in the life and teachings of the one who made himself nothing, taking the very form of a servant," the Queen said.
In her address, the Queen said the place of religion had come to be a matter of "lively discussion" in a more "diverse and secular" society.
"It is rightly acknowledged that people of faith have no monopoly of virtue and that the well-being and prosperity of the nation depend on the contribution of individuals and groups of all faiths and none," she said.
"Yet, as the recent visit of His Holiness the Pope reminded us, churches and the other great faith traditions retain the potential to inspire great enthusiasm, loyalty and a concern for the common good."
The Queen's address came after she attended a service of Holy Communion at Westminster Abbey to inaugurate the new General Synod.
Dame Mary Tanner, a president of the World Council of Churches, who gave the sermon at the service, warned the Synod against becoming "inward looking" or "obsessed" with its own internal life.
"You are to help us to be more firm in our faith, more convincing in making Christ known in a hurting world, more attentive to the poor and vulnerable, more self-sacrificial in our service, more dynamic in our missionary task, as we walk together on the way," she said.