Intestinal malrotation (IM) results from an altered or incomplete rotation of the fetal midgut around the superior mesenteric artery axis. The abnormal anatomy of IM is associated with risk of acute midgut volvulus which can lead to catastrophic clinical consequences. The upper gastro-intestinal series (UGI) is addressed as the gold standard diagnosis procedure, but a variable failure degree has been described in literature. The aim of the study was to analyze the UGI exam and describe which features are the most reproducible and reliable in diagnosing IM. Medical records of patients surgically treated for suspected IM between 2007 and 2020 at a single pediatric tertiary care center were retrospectively reviewed. UGI inter-observer agreement and diagnostic accuracy were statistically calculated. Images obtained with antero-posterior (AP) projections were the most significant in terms of IM diagnosis. Duodenal-Jejunal Junction (DJJ) abnormal position resulted to be the most reliable parameter (Se = 0.88; Sp = 0.54) as well as the most readable, with an inter-reader agreement of 83% (k = 0.70, CI 0.49–0.90). The First Jejunal Loops (FJL), caecum altered position and duodenal dilatation could be considered additional data. Lateral projections demonstrated an overall low sensitivity (Se = 0.80) and specificity (Sp = 0.33) with a PPV of 0.85 and a NPV of 0.25. UGI on the sole AP projections ensures a good diagnostic accuracy. The position of the third portion of the duodenum on lateral views showed an overall low reliability, therefore it was not helpful but rather deceiving in diagnosing IM.