Side-to-side intestinal anastomosis is a surgical procedure where an incision is performed between two parallel segments of gut and then they are sutured together. The purpose of this paper is to investigate if the standard surgical practice diameter used in anastomosis leads to undesirable closed circulatory flows which may be harmful to the gut tissue. A finite element model for the chyme flow in a side by side anastomosis with realistic user configurable parameters is developed and solved in a wide range of situations. We analyze the flow crossing the anastomosis, the normalized pressure difference in the gut section and the streamlines that show the presence or absence of closed flow regions for a set of surgically feasible anastomosis diameter values. In contrast with the findings of simpler analytical models, closed flows do not appear in any of these cases. The study shows that the current standard surgical practice where the anastomosis diameter is similar to the gut diameter does not lead to undesirable effects predicted by some simple analytical models.