Shakespeare’s father, John, was identified in 1592 as a recusant, a Catholic who refused to attend the services of the Church of England. However, no one has firmly established why he missed the services. The possibility exists that his absence was due to reasons unconnected with his religious beliefs. On the other hand, one may fairly ask why he was accused of recusancy instead of simple truancy. Of course, one may also fairly ask whether William Shakespeare would have followed the example of his father if the latter had remained Catholic.

2...Mary Shakespeare's Catholicity

Shakespeare’s mother, Mary Arden Shakespeare, belonged to a fiercely loyal Catholic family not far from Stratford. A member of that family, Edward Arden (whose father was a cousin of Mary), befriended Catholics—including a priest named Hugh Hall, who lived in disguise on Edward Arden’s property—and opposed the religious policies of the Crown. The government eventually caught up with him and accused him of plotting against the queen. He was executed him in 1583, and his head was impaled on a stake atop London Bridge. However, this evidence fails to demonstrate that Mary Arden Shakespeare was as fixed in her religious views as Edward Arden. If she had decided to bend to the will of the Crown rather than to follow the example of Edward, William might well have decided to walk in her footsteps.

3...William Shakespeare's Schooling

When he was an elementary student at the King’s New School in Stratford, William Shakespeare’s schoolteachers included at least two Roman Catholics, Simon Hunt and John Cottom, who may have taught or promoted Catholic ideas. A third teacher, Thomas Jenkins, may also have been a Catholic. However, Shakespeare’s plays suggest that as a boy he used the Protestant Geneva Bible, published in English on the European continent between 1557 and 1560 and in England in 1576. It is possible that Shakespeare was also familiar with the first English translation of the Catholic Bible, the Douay-Rheims version. The New Testament of that Bible became available in England in 1582 and the Old Testament, between 1609 and 1610.

4...William Shakespeare's Wedding 

John Frith, who presided at Shakespeare’s marriage to Anne Hathaway in 1582 in the village of Temple Grafton (about four miles from Stratford), was identified by the government in 1586 as a Roman Catholic priest even though he had outwardly affected Protestant ways. It is reasonable to speculate, therefore, that Shakespeare chose the church in Temple Grafton as the site of his wedding, not the then Protestant church in his hometown, because he wanted to marry in a Catholic ceremony. 

5...Shakespeare and Southwell: Were They Spiritual Kin?

See Topcliffe: Elizabeth's Reichsführer, above.

6...The Mysterious Document Hidden in the Rafters

A document found in John Shakespeare’s home—in which William lived as a boy and a teenager, then as a married man with his wife until 1597, when he bought his own home in Stratford—contained wording identical to that in a pamphlet distributed by Edmund Campion (1540-1581), a Jesuit priest. The pamphlet was an English translation of an Italian document written by the Catholic Archbishop of Milan, Charles Borromeo (1538-1584). Borromeo (in Italian, Carlo Borromeo), a member of the religious society of Oblates of St. Ambrose (known today as the Oblates of St. Charles), was a major figure in the Catholic Counter-Reformation, a movement to combat the Protestant Reformation. His pamphlet was a deathbed profession of faith used to hearten persecuted Catholics in Europe. Campion pretended to be a jewel merchant while distributing the pamphlet and ministering and preaching to English Catholics at clandestine meetings, including gatherings less than 15 miles from Stratford. The found document in the Shakespeare home—a John Shakespeare's will with the pamphlet wording appended—was discovered on April 29, 1757, by a bricklayer. It was stuffed between rafters and the roof covering. The owner of the home at that time was John Hart, a descendant Joan Shakespeare, William's sister, and Joan's husband, William Hart. If the pamphlet was authentic and if it was hidden by John Shakespeare, it would link him directly or indirectly with Campion, who was tortured and executed in 1581 for promoting Catholicism and denouncing the Church of England. William Shakespeare was living in his father’s home (on Henley Street in Stratford) at the time of Campion’s campaign and likely would have known about the will. Whether he would have approved of the religious message in it is arguable. 

7...Was Shakespeare "Shakeshafte"?

As a teenager, William Shakespeare may have practiced the Catholic faith under the name "William Shakeshafte" while working for and living with Alexander Hoghton (also spelled de Hoghton and Houghton) and his family in a sprawling, castle-like manor house in northwest England near the towns of Preston, Blackburn, and Darwen in the county of Lancashire. Known as Hoghton Tower and alternately Hoghton Castle, the manor house was a hotbed of Catholic activity, with priests (such as Edmund Campion) or aspiring priests using it as a kind of way station while traveling to and from the European continent. That Shakespeare was an employee (a servant or perhaps a tutor of children ) in the Hoghton household is based on the following information: 

A...Hoghton identified William Shakeshafte as an employee of his. 
B...William Shakespeare's grandfather, Richard, once used the name Shakeshafte.
C...William Shakeshafte's initials, W.S., were the same as William Shakespeare's
D...Shafte is an Elizabethan spelling variation of shaft, and speare is a variation of spear. Dictionaries define shaft in primary definitions as the cylindrical part of a spear, or the spear itself. Hence, Shake and shafte could represent Shake and speare, or Shakespeare.
E..John Cottom, one of William Shakespeare's teachers at the King's New School in Stratford, was an acquaintance of Alexander Hoghton. Cottom's brother was tortured and executed for espousing the Catholic cause...
F..Edmund Campion, a Catholic priest who distributed a pamphlet with a message repeated in the will of William Shakespeare's father, was among the Catholic visitors to Hoghton Tower.
G..Hoghton maintained a private theater, costumes, and musical instruments for staging plays. 
H..In his will, Hoghton bequeathed his theater paraphernalia to his brother-in-law, Thomas Hesketh, in the event that Hoghton's brother, Thomas, had no use for them. Hoghton also recommended that Hesketh accept Shakeshafte in his service.
I..Hesketh once took a group of actors to the home of the Earl of Derby. The earl's son, Lord Strange, maintained a company of actors.
J..In London, Shakespeare was believed to have first worked for an acting company called Lord Strange's Men, according to the Encyclopedia Britannica.
K..One of the financial backers of the Globe Theatre, in which Shakespeare held part ownership and staged many of his most famous plays, was Thomas Savage, who had resided in Lancashire and married a member of the Hesketh family. (See H and I, above.)

The evidence in Points A to K above has been discussed by various writers over the years. In 1923 Edmund Chambers was the first researcher to consider the possibility that Shakeshafte was Shakespeare. In a 1937 book, Shakespeare's Warwickshire and the Unknown Years, Oliver Baker, of Stratford, pursued this theory. Chambers continued his research after the Baker book, and many other researchers—including Ernst A.J. Honigmann, in Shakespeare: The Lost Years—followed up on the research of both Edmunds and Baker. The combined research indicates that the Hoghton home was a safe house for Catholics, where William Shakespeare (if he indeed worked there) could practice Catholicism—or at least retain Catholic beliefs—without fear of discovery. Daring theorists have even suggested that William himself originally intended to go to the European continent to study for the priesthood. 
. .
8...The Gunpowder Plot and a Possible Shakespeare-Campion Connection

In November 1605, defiant recusants plotted to kill King James I, the queen, their oldest son, and members of Parliament by exploding barrels of gunpowder beneath the House of Lords and the adjacent royal palace. However, before the conspirators could execute their plan—scheduled for Nov. 5—government authorities arrested one of the plotters, Guy Fawkes, after receiving a tip. They tortured him until he disclosed the details of the conspiracy, which became known in English history as the Gunpowder Plot. What makes this incident relevant in research about Shakespeare's religion is that the leader of the conspiracy, Robert Catesby (1573-1605), and other conspirators lived in the Stratford region. Catesby's father, Sir William Catesby, once hosted Edmund Campion (1540-1581), the Jesuit priest mentioned in Numbers 6 and 7 above, at the Catesby home in Lapworth, Warwickshire. There is speculation that William Shakespeare once met Campion and approved of his activities.

9...The Empty Pew

Although the English government maintained records of persons attending Protestant services, no records exist indicating that William Shakespeare registered as a member of the Church of England, as required, while he lived off and on in London. 

10...The Empty Pew 2: Shakespeare's Daughter Identified as a Recusant

On May 5, 1606, the government identified Shakespeare’s daughter Susanna as a recusant for failing to attend an Easter service of the Church of England at which she was supposed to receive holy communion. If Susanna was indeed a recusant, one may fairly speculate that her father, William, reared her a Catholic. Of course, it is possible she was her own guiding star on matters of conscience—or missed the Easter service because she was suffering from a bad headache.

11...Blackfriars Gatehouse: Catholic Haven or Investment Property?

On March 10, 1613, Shakespeare purchased Blackfriars Gatehouse on Puddle Dock Hill in London from Henry Walker for £140. Presumably, Shakespeare planned to rent the property and perhaps live there during his last days as a London playwright. However, the gatehouse was said to be a hiding place for London Catholics, complete with tunnels. Whether Shakespeare bought the property to aid Catholics or to augment his income and provide lodging for himself cannot be determined. The Folger Shakespeare Library in Washington, D.C., holds Shakespeare's copy of the deed of purchase for the gatehouse.

12...Anglican Minister's Testimony

A statement affirming that Shakespeare died a Catholic was written, ironically, by an Anglican minister, Archdeacon Richard Davies, of Gloucestershire. In the late 1600's, he wrote notes added to a reference work—a collection of biographies written by the Rev. William Fulman—that said Shakespeare "dyed a Papyst [died a Papist]." A Papist was a Catholic loyal to the pope and the church of Rome. However, the reliability of Davies' information is dubious, for in the same notes he also says Shakespeare in his youth stole deer and other animals from the property of Sir Thomas Lucy (1532-1600) of Charlecote, Warwickshire. Many Shakespeare scholars (but not all of them) have since labeled this story apocryphal. According to an article first published in 1918 in Old and Sold Antiques Digest, the Fulman manuscript is in the possession of Oxford University's Corpus Christi College.

13...Shakespeare's Plays and Their Catholic Characters 

Numerous passages in Shakespeare’s plays indicate that he had a deep understanding of Catholicism, its tenets, and its rituals. Moreover, he often cast Catholic characters in a favorable light in conflicts involving moral principles, unjust traditions and practices, and theological and philosophical issues. Among these Catholic characters and the plays in which they appear are Hamlet, in Hamlet, Prince of Denmark; Aemilia, the abbess in The Comedy of Errors; Friar Laurence, in Romeo and Juliet; Friar Francis, in Much Ado About Nothing; and Thomas More, in Sir Thomas More (a play believed to be of joint authorship, with passages written or revised by Shakespeare). However, Shakespeare also depicted Catholic characters in an unfavorable light, including Joan of Arc, in Henry VI Part I; Cardinal Thomas Wolsey, in Henry VIII; the Archbishop of Canterbury and the Bishop Ely, in Henry V; and the heartless aristocrats in The Merchant of Venice, who ridicule Shylock, a Jewish moneylender, and force him to become a Christian.

14...Shakespeare's Outcasts: Catholic Surrogates? 

Shakespeare populates many of his plays with outcasts. If Shakespeare had clung to Catholicism, he may have been using these outcasts to symbolize his own status as a religious pariah. Among his outcast characters and the plays in which they appear are Duke Senior and his outlaws, in As You Like It; Prospero, in The Tempest; Posthumus Leonatus, in Cymbeline; Timon, in Timon of Athens; and Cordelia, the Earl of Kent, and Edgar, in King Lear. It is even possible (if one wishes to delve further into sheer speculation) that Shakespeare deliberately made Shylock, the Jewish moneylender in The Merchant of Venice, a sympathetic character because of his outcast religious status. Few Jews lived in England in Shakespeare’s time, for the government had expelled everyone espousing the Jewish faith under a 1290 decree. However, a small number of Jews remained in England over the centuries, pretending to accept Christianity. In the Elizabethan and Jacobean eras, publicly professing Christianity meant a Jew had to pledge allegiance to the Church of England, like a Catholic.