Olivia and Micah Gee, 2 and 3 respectively, were put to bed around 8:30 p.m. in their Van Cortland Park South home, near Orloff Avenue, sources said.
Their mom's boyfriend went to check on the pair, who have a history of asthma, about 1:30 a.m. and noticed them having trouble breathing, sources said.
They were brought to Montefiore Medical Center where they were pronounced dead, police said.
It wasn't immediately clear how the two died, police said.
ACS officials are investigating their deaths, but declined to elaborate, citing confidentiality laws.
The Medical Examiner will determine their cause of death, police said.
Neither child showed any signs of trauma, police said.
The family doesn't have prior interactions about domestic incidents with police, an NYPD spokeswoman said.