Q&A: My afp results came back fine, but after taking an ultrasound, I was told that my baby had a marker for Down Syndrome called an Ecogenic Bowel.

It is unclear whether you had the maternal serum triple or quadruple screen for conditions such as Spina Bifida and chromosome abnormalities including Down Syndrome. You may want to refer to my response to a question on this subject a few weeks back.
The appearance of a hyper-intense spot in the fetal intestine raises a question about the potential presence of a chromosome abnormality or cystic fibrosis affecting the fetus. Each of these two possibilities are associated with low risks, each approximating 1%.
The risk of fetal loss due to an amniocentesis approximates 0.5 to 1.0%. Hence, any decision to have an amniocentesis would have to balance these two risks and the parents' wishes to exclude a chromosome defect. The possibility of cystic fibrosis in the fetus would call for a DNA test on both parents first to determine if a mutation (defect) in the cystic fibrosis gene could be determined. If there is no time left for parental testing, then a direct test on fetal cells cultivated from the amniotic fluid and obtained at the time of amniocentesis could be used for DNA mutation analysis of the gene for at least the most common defects (I also answered a question on Cystic Fibrosis a few weeks back).
Remember, the triple or quadruple maternal serum test is simply a screen, not a diagnosis and cannot be used for great reassurance since at least 20% of chromosome defects will be missed by this screen.