The 30-year-old had nothing to say when the charges were put to him by the arresting officer.
The homeless man, who has been in custody since Saturday night, appeared before Longford district court this morning.
The accused was brought into the court house just before 9am in a white van flanked by the garda armed support unit.
Up to 50 people shouted abuse as he was taken from the court.
The victims of the alleged assault, aged just six and nine, were attending a birthday party in Athlone on Saturday afternoon when they went missing.
He was escorted into the courtroom at 10.36am where he appeared before Judge Seamus Hughes. During the 10-minute hearing, Inspector Yvette McCormack gave evidence of arresting the defendant at 6.54pm on Monday in Athlone Garda station and charging him at 7.45pm.
The court heard that when each of the four charges were put to him he made no reply.
Dressed in blue jeans, white runners and a black jacket, the defendant, who had a scrape on the left side of his face, stood quietly in the body of the courtroom where he did not speak.
Judge Hughes granted legal aid for the accused who is unemployed. He also requested a psychiatric evaluation following a request by defence solicitor Gearoid Geraghty.
"I have concerns with regards to my client's ability to enter a plea," he told the court.
The defendant, of no fixed abode, was remanded in custody to appear before Harristown District Court this Friday.
Mr Geraghty said that no application for bail was being contemplated. The judge accepted a request that the accused be kept on suicide watch while in custody
He also requested that the defendant recieve any appropriate medical attention, referencing the mark on his face.
He called for the usual protections for the defendant while in custody.
Mr Geraghty raised a concern about about he saw as pre-trial predujicial media reports concerning his client. The judge reminded the media of their duty in the case in preserving the anonymity of both the defendant and the alleged victims. The alleged rape of a six and nine-year-old girl occurred on Saturday afternoon. They had been attending a birthday party in the town when they went missing.
There was up to 30 garda officers both inside and outside the court while the proceedings were under way.
Up to 25 members of the public were gathered at the back of the court while the accused man was brought in and out of the building.