Manish Shah, from Romford area of London, had been charged with 65 counts of assault by penetration and 52 allegations of sexual assault by Scotland Yard earlier this month.
"Shah is also charged with one count of sexual assault on a girl under the age of 13," the Metropolitan Police said. Barkingside Magistrates' Court in east London was told that he denied all the charges against him.
Judge Richard Hawgood granted him conditional bail and set September 27 as the date for his next court appearance at a plea and case management hearing at Snaresbrook Crown Court in north-east London.
"These are matters that can only be dealt with in the crown court, or they are matters that are linked to matters that can only be heard at crown court," Judge Hawgood said.
The court was told that Shah has been suspended from practising as a general practitioner (GP) by the UK's General Medical Council (GMC) and is barred from accessing medical records held by the country's state-funded National Health Service (NHS).
His bail condition states that he must not attend his former surgery in east London or contact any current or former patients of the surgery or any of its past or current employees.
The offences are alleged to have taken place at a medical practice in Havering, Romford, between June 2004 and July 2013, when he was first arrested.
Scotland Yard had launched an investigation after several people contacted the police in July and August 2013.
"Manish Shah has been charged with 65 assault by penetration, contrary to Section 2 of the Sexual Offences Act 2003, 52 sexual assault, contrary to Section 3 of the Sexual Offences Act 2003, and 1 sexual assault on a child under 13 years, contrary to Section 7 of the Sexual Offences Act 2003," the Met Police said in a statement.
Shah is a family planning specialist who trained at St Bartholomew's Hospital in London and qualified in 1993.
Until recently, he was listed as working in a limited capacity at a GP surgery in Southend-on-Sea, Essex. The alleged offences do not relate to his time at that particular practice in the east of England.