Size The holotype of
Scipionyx represents a very small individual, the preserved length of which is estimated at just . In 2011, dal Sasso and Maganuco estimated its total length, including the missing tail section, at . The specimen was not much smaller than known embryos or hatchlings of
Lourinhanosaurus and
Allosaurus, theropods of considerable magnitude. However, given its affinities with the
Compsognathidae, it is likely that the adult size of
Scipionyx did not surpass that of the largest known compsognathid,
Sinocalliopteryx, which itself measures in length. As the hatchling would have fitted within an egg about long and wide, this would have implied a rather high egg size compared to the adult body length.) or an intestine (
Mirischia,
Daurlong) have been reported from other dinosaurs,
Scipionyx is unique in preserving in some form examples from most major internal organ groups: blood, blood vessels, cartilage, connective tissues, bone tissue, muscle tissue, horn sheaths, the respiratory system and the digestive system. Nervous tissue and the external skin, including possible scales or feathers, are absent. The soft tissues are not present in the form of imprints but as three-dimensional petrifications, having been replaced by
calcium phosphate in amazing detail, even to the subcellular level; or as transformed remains of the original biomolecular components.
Bone tissue The original bone tissue is no longer present but the calcium phosphate mineralisation has preserved the structure of original bone cells, showing individual
osteocytes including their inner hollow spaces and the
canaliculi. Also the internal blood vessels of the bone have been preserved, in some cases still empty inside. On some bones, including some of the skull and lower jaws, the
periosteum is still visible.
Ligaments and cartilage From the ninth cervical vertebra to the back, the vertebral joints show the remains of
articular capsules. Between the spines at places very thin interspinal and supraspinal
ligaments are visible. Six vertebrae are visibly capped by cartilaginous synchondroses, a typical juvenile feature. Cartilaginous caps are also present on all limb joints, even the smallest, and are especially thick in the shoulder, elbow and wrist joints. Also the pubic foot is capped and the ilium and pubic bone are separated by cartilage.
Respiratory system Of the
respiratory system little has been preserved. No traces of the lungs have survived, nor of any air sacks. The sole element still present consists of a seven millimetre long piece of the
trachea of which about ten tracheal rings are visible, the most anterior of which are open at the top, giving them a C-shape. They have an average length of 0.33 millimetres and are separated by 0.17 millimetre thick interspaces. The trachea is quite thin, with a preserved width of one millimetre about half as wide as would be expected for an animal the size of the holotype, and positioned rather low in the neck base, embedded in connective tissue.
Liver, heart, spleen and thymus In the front part of the
thorax a conspicuous red halo is visible, forming a roughly circular stain with a diameter of seventeen millimetres. In 1998 it was suggested this might represent the remains of the decayed
liver, a blood-rich organ. That the red pigment was indeed derived from blood, was confirmed in 2011: a
scanning electron microscope analysis indicated that the substance consisted of
limonite, hydrated
iron oxide, a likely transformation product of the original
haemoglobin. Also
biliverdine was present, a
bile component expected in the liver. The blood might also partly have originated from the
heart and the
spleen, two similarly blood-rich organs, with reptiles positioned between the two lobes of the liver. Another organ in the thorax, traces of which might be present, is the
thymus, which might have contributed to a greyish mass of organic origin visible in the neck base; this also contains connective and muscle tissue.
Digestive system The
digestive tract can mostly be traced, either because the intestines are still present or by the presence of food items. The position of the
oesophagus is indicated by a five millimetre long series of small food particles. Below the ninth dorsal vertebra the location of the stomach is shown by a cluster of bones of prey animals, the organ itself likely having been dissolved by its own
stomach acid shortly after death. The rather backward position of the cluster suggests the stomach was dual in structure, with a forward
enzyme-secreting
proventriculus preceding a muscular
gizzard.
Gastroliths have not been reported. Just behind the presumed position of the stomach a very conspicuous large and thick intestine is visible, that has been identified as the
duodenum. It is preserved partly in the form of a natural
endocast, partly as a petrification still showing the cellular structure, including the
mucosa and connective tissue. Some
mesenteric blood vessels cover the intestine in the form of up to a centimetre long and 0.02 to 0.1 millimetre wide hollow tubes. The duodenum forms a large loop, the descending part of which first is directed downwards towards the gastralia and then runs to the back. There in a sharp bend, the folds of which are clearly visible, it turns to the front, proceeding as an ascending tract, its visible part ending near the stomach. At this point the tract is directed to the left of the body, perpendicular to the fossil slab, and its course can thus no longer be followed. Nearby and slightly above, a subsequent intestine part surfaces that has been interpreted as the
jejunum. This thinner intestine turns to the back, running parallel to the ascending tract of the duodenum and ultimately disappearing under it, at the level of the twelfth dorsal vertebra. Apparently a loop to the front is made because it resurfaces below the tenth dorsal vertebra, first running upwards and then turning to the back below the hind vertebral column — or at places even over it: probably after death its position partly shifted upwards. The jejunum seems to blend with an exceptionally short
ileum. A contraction below the thirteenth dorsal vertebra might indicate the transition to the
rectum. A
caecum seems absent. The rectum runs to the back between the upper shafts of the pubes and ischia. Then it bends downwards parallel to the ischium shaft, at the end of it turning upwards again. In this final part
faeces are still present. The
cloaca is lacking. Dal Sasso & Maganuco suggested the cloaca exit was rather low, at the level of the ischial feet and that a
rectocoprodaeal valve separated faeces and urine. Between the front edge of the pubic shafts and the back of the intestines a large empty space is present. Also, the rectum seems to run in a very high position as if it were forced upwards by something. According to Dal Sasso & Maganuco, in life this space would have been filled by the
yolk sac of the hatchling; on hatching the juveniles of reptiles typically have not absorbed all the yolk and use the residual nutrients to supplement the food intake during their first weeks.
Muscle tissue At several places on the fossil
muscle tissue is present. The degree of preservation is often exceptional, with not only the individual fibres still discernible but also the individual cells and even the subcellular
sarcomeres. Among dinosaur fossils such sarcomeres are only known from
Santanaraptor, whose muscle fibres are four times as thick. The original organic material has been replaced by small hollow globes, the walls of which consist of
euhedric crystals of
apatite. In the grey organic mass at the neck base, muscle fibres are present that have been identified as belonging to the
Musculus sternohyoideus and the
Musculus sternotrachealis. Between the sixth and seventh dorsal vertebra a patch of muscle fibres is visible belonging to either the
Musculus transversospinalis or the
Musculus longissimus dorsi. In front of the right ischium muscle fibres are present running from the ischial foot in the direction of the femur. Their identity is uncertain: they could belong to the
Musculus puboischiofemoralis pars medialis (the
Musculus adductor femoris I of crocodiles) but in that case this muscle with (some) non-avian theropods would not be anchored on the obturator process. The fibres could also represent an unknown muscle. In any case they refute a conjecture by
Gregory S. Paul that there would be no muscle connection between the ischium and the femur at all. Above the rectum tract a large area of horizontal unsegmented muscle fibres is present, probably representing the unsegmented
Musculus caudofemoralis longus of the tail base, the main retractor muscle operating on the thighbone. These fibres are polygonal in cross-section and show the intercellular spaces also. Below some tail base vertebrae the connective ligaments between the chevrons are present, forming the
ligmamentum interhaemale, but also some small muscle fibres and some mysterious hollow tubes arranged in a herringbone pattern; the latter perhaps represent the
myosepta of the
myotomes, the segments of the
Musculus iliocaudalis or the
Musculus ischiocaudalis.
Horn sheaths On all claws preserved in the fossil — those of the feet have all been lost — horn sheaths are visible. These have a darker colouration on top than on the bottom which suggests that the original horn material is still present — but this has not yet been directly tested by a chemical analysis for fear of damaging these delicate structures that were seen as forming an essential part of the integrity of the precious specimen. The horn sheaths of the hand claws extend the bony cores by about 40%, scythe-like continuing the bone curve and ending in sharp points. On some claws the sheaths have partly detached; on others they have been flattened or split.
Integument The fossil preserves no traces of any skin, scales or feathers. In 1999
Philip J. Currie hypothesised this might be otherwise, suggesting the tubes found on the tail base would represent the filaments of protofeathers. In 2011, however, Dal Sasso & Maganuco rejected this interpretation because the tubes taper at both ends, while integument filaments are expected to have only a tapered top end. Nevertheless, they considered it likely that
Scipionyx in life had protofeathers as these are known to be present with the compsognathids
Sinosauropteryx and
Sinocalliopteryx. == Phylogeny ==