Researchers at Britain's Bristol University say it reveals a universe of detail impossible using previous methods and is pushing back the frontiers of science much as the scanning electron microscope did half a century ago.
"We are looking at the dawn of life," lead researcher Phil Donoghue said.
"Because of their tiny size and precarious preservation, embryos are the rarest of all fossils."
"But these fossils are the most precious of all because they contain information about the evolutionary changes that have occurred in embryos over the past 500 million years."
In contrast to existing methods of exterior observation or destructive sectioning of fossil embryos, synchroton-radiation X-ray tomographic microscopy (SRXTM) leaves the tiny fossils untouched but gives graphic details of their structure.
The team used a 500m wide particle accelerator in Switzerland to deep scan the minute fossils and then fed the information into a computer which generated complete three-dimensional images of the internal structures in fine detail.
"The best analogy is with a medical CT scan ... but at 2-3,000 times the resolution," Donoghue said. "We can see details less than 1,000th of a milimetre in dimension.
"We can look at any and every part of the fossil - inside and out - without harming it and then virtually dissect it however we like."
The team, who published their findings in the science journal Nature, said their discoveries could roll back the evolutionary history of arthropods like insects and spiders.
In one case they had found hitherto hidden details of the interior structure of an ancient relative of the living penis worm, and in another they had seen embryonic worm segments unlike those found in living specimens today.
"SRXTM provides a non-invasive method of analysis of small and microscopic fossil materials ... unlocking the finest details of preserved anatomy from fossilised remains," they wrote.
"The method has wide applicability in the study of microscopic structures ... and may thus bring about a revolution in palaeontology on a par with that once brought about by the scanning electron microscope."