To each charge came the same reply: "Not guilty, your honour."
The former military medical technician faces 26 sexual assault and breach of trust charges involving 16 women over a six-year span.
The charges allege inappropriate medical exams at Ontario military recruitment sites in Thunder Bay and London from 2003 to 2009.
Among the allegations against Wilks are that he had women expose their breasts, and that he touched their breasts during medical exams, the court martial heard Wednesday.
He was told that it was not his job to conduct breast exams, the court martial also heard.
"At the end of this case, the evidence will show that petty officer second class Wilks conducted these examinations in a manner contrary to the policies and procedures for these examinations," said military prosecutor Maj. Dylan Kerr, "and that in doing so, he used his position of authority and trust to violate the privacy rights and sexual integrity of these women for his own gratification."
None of the allegations have been proven in court.
Wilks, a petty officer second class who is now retired, was originally charged with 11 counts of sexual assault and 18 counts of breach of trust under the National Defence Act.
But three of those charges involving two of the women were withdrawn Wednesday.
Wilks said nothing as he walked into the courtroom wearing a dark suit, red tie and sunglasses.
Outside the court, Kerr underscored the seriousness of the charges.
"Petty officer Wilks was entrusted with a particular role in an official capacity," Kerr said. "So we take that quite seriously."
Maj. David Hodson, the lawyer representing Wilks, cautioned against rushing to judgment.
"Petty officer second class Wilks is entitled to a presumption of innocence, and he will not be convicted until the prosecution presents enough innocence that the judge is satisfied beyond a reasonable doubt to convict him," Hodson said outside court.
Most of the first day of Wilks' court martial, which is expected to take three weeks, was lost to procedural delays. There was a drawn-out discussion about whether or not to release a document to the media listing the charges against Wilks. Eventually the judge agreed to release it with the withdrawn charges blacked out.
Military judge Lt.-Col. Louis-Vincent d'Auteuil also granted Kerr's request for a publication ban on any information that might identify some of the women making the allegations.
Wilks also faces separate civil lawsuits that claim the military didn't act on reports about his alleged conduct.
Three women filed statements of claim with the Ontario Superior Court of Justice alleging that Wilks sexually assaulted them during physical exams for recruits at various National Defence installations in Ontario.
A fourth woman last year filed a similar civil claim against Wilks. It alleges he touched her breasts and pressed his groin against her during a recruitment medical exam.