He had expected to see mites or amoebas, perennial pests of bees. Instead, he found internal organs swollen with debris and strangely blackened. The bees' intestinal tracts were scarred, and their rectums were abnormally full of what appeared to be partly digested pollen. Dark marks on the sting glands were telltale signs of infection.
"The more you looked, the more you found," said VanEngelsdorp, the acting apiarist for the state of Pennsylvania. "Each thing was a surprise."
VanEngelsdorp's examination of the bees in November was one of the first scientific glimpses of a mysterious honeybee die-off that has launched an intense search for a cure.
The puzzling phenomenon, known as Colony Collapse Disorder, or CCD, has been reported in 35 states, five Canadian provinces and several European countries. The die-off has cost U.S. beekeepers about $150 million in losses and an uncertain amount for farmers scrambling to find bees to pollinate their crops.
Scientists have scoured the country, finding eerily abandoned hives in which the bees seem to have simply left their honey and broods of baby bees.
"We've never experienced bees going off and leaving brood behind," said Pennsylvania-based beekeeper Dave Hackenberg. "It was like a mother going off and leaving her kids."
Researchers have picked through the abandoned hives, dissected thousands of bees, and tested for viruses, bacteria, pesticides and mites.
So far, they are stumped.
According to the Apiary Inspectors of America, 24% of 384 beekeeping operations across the country lost more than 50% of their colonies from September to March. Some have lost 90%.
"I'm worried about the bees," said Dan Boyer, 52, owner of Ridgetop Orchards in Fishertown, Pa., which grows apples. "The more I learn about it, the more I think it is a national tragedy."
At Boyer's orchard, 400 acres of apple trees -- McIntosh, Honey Crisp, Red Delicious and 11 other varieties -- have just begun to bud white flowers.
Boyer's trees need to be pollinated. Incompletely pollinated blooms would still grow apples, he said, but the fruit would be small and misshapen, suitable only for low-profit juice.
This year, he will pay dearly for the precious bees -- $13,000 for 200 hives, the same price that 300 hives cost him last year.
The scene is being repeated throughout the country, where honeybees, scientifically known as Apis mellifera, are required to pollinate a third of the nation's food crops, including almonds, cherries, blueberries, pears, strawberries and pumpkins.
One of the earliest alarms was sounded by Hackenberg, who used to keep about 3,000 hives in dandelion-covered fields near the Susquehanna River in Pennsylvania.
In November, Hackenberg, 58, was at his winter base in Florida. He peeked in on a group of 400 beehives he had driven down from his home in West Milton, Pa., a month before. He went from empty box to empty box. Only about 40 had bees in them.
"It was just the most phenomenal thing I thought I'd ever seen," he said.