Mark Bridger's voice faltered when he was asked if he understood the charges against him and tears welled up in his eyes.
Dozens of members of the public stood in the rain outside Aberystwyth magistrates court in mid-Wales to hurl abuse – and a bottle – at the security van that he was taken to and from court in.
Bridger, 46, was told the next hearing would be at Caernarfon crown court in north Wales on Wednesday. He is due to appear via videolink from prison in Manchester.
Meanwhile, April's mother, Coral Jones, issued a fresh appeal for help in finding her daughter, who has not been seen since she disappeared as she played near her home in Machynlleth last Monday evening.
In a message posted on Facebook, she said: "April has still not been found, I am not giving up hope that she will come home, so please keep looking for my baby girl April. She's our world, the whole family are in bits as we don't know where she is."
Police have said they are continuing to search for the missing girl, who had been allowed to play out late as a treat after her parents received a glowing report about her progress at school.
On Sunday as many as 1,000 people attended a special service at St Peter's church in Machynlleth to pray for the girl and her family.
A much smaller crowd – around 30 people – gathered in the drizzle to watch as the van carrying Bridger arrived. One man, who had travelled from Birmingham, threw a plastic bottle of energy drink at the vehicle and others hurled abuse.
His case was heard in court one, which overlooks Aberystwyth marina.
Three seats were reserved for members of April's family who wished to attend but they remained empty.
Two plain-clothes police officers sat in the body of the court together with Superintendent Ian John, whose duties over the last week have included explaining the search efforts to the people of Machynlleth and the media.
Wearing a tight-fitting blue sweatshirt and dark trousers, Bridger was led into the dock flanked by two security guards. He was not wearing handcuffs but kept his hands behind his back. It was the first time he has been seen in public since he was arrested last Tuesday.
Asked if he was Mark Leonard Bridger, he replied: "That is correct." He paused when he was asked what his address was and the clerk read it out: "Mount Pleasant Cottage, Ceinws." Bridger simply said: "Correct."
He confirmed his date of birth and was told the severity of the charges meant he could not be tried in a magistrates court.
The first charge – the murder of April Sue-Lyn Jones between 30 September 2012 and 3 October 2012 – was detailed. He looked to the ceiling and tears welled in his eyes.
He bit his lip and answered "yes" in a trembling, high-pitched voice when he was asked if he understood the charge.
Bridger is also charged with the abduction of April on 1 October and the unlawful disposal and concealment of her body with intent to pervert the course of justice between 30 September and 3 October.
To both those charges, Bridger replied simply: "Yes", in the same high-pitched voice, when asked if he understood the allegations.
The chair of the bench, Betty Griffiths, asked him to take a seat and Bridger was told that he would be remanded in custody until Wednesday when his case will be heard at Caernarfon crown court.
Outside the crowd had swollen to around 50. They had a wait of more than hour in the rain because Bridger was given breakfast in the cells before the long drive.
As the van left, the same bottle of energy drink, which had been recovered earlier, was thrown at the van. Police held people back as they tried to get at the vehicle but one man banged the side, shouting abuse.
Away from court, the Welsh secretary, David Jones, hailed the "tremendous community spirit" of the people of Machynlleth.
Addressing the Conservative party conference, he asked activists in Birmingham to "spare a few thoughts today for April Jones, her family and the officers of Dyfed-Powys police and the search and rescue services".
He added: "Most particularly, could I ask you to think about the people of Machynlleth who, over the last seven really harrowing days, have displayed such tremendous community spirit."
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