Mark Bridger has been taken into custody after leaving Aberystwyth Magistrates' Court.
The 46-year-old faces three charges of murder, abduction and perverting the course of justice.
At the end of the hearing Betty Griffiths, the chairman of magistrates, told Bridger he would be remanded in custody and would next appear at Caernarfon Crown Court on Wednesday.
John Hedgecoe was defending Bridger. Iwan Jenkins, district crown prosecutor, was prosecuting. Neither were called upon to speak during the brief hearing.
Also sitting at the back of the court was Superintendent Ian John, who has led the search for April.
Afterwards he returned to Machynlleth to continue co-ordinating the on-going search operation.
Police say they have almost finished searching April Jones' home town and the focus has shifted to suspect Mark Bridger's village.
Police have confirmed the high numbers of officers searching for April Jones will remain over the weekend.
Mark Bridger appeared in court this morning accused of the abduction and murder of five-year-old April Jones.