Vesicular swelling in the cervical region (VSC) is occasionally observed among human embryos around Carnegie stage (CS) 21. However, its mechanism and significance in fetal development are unclear. The present study aimed to analyze the relation of development of VSC with jugular lymph sac (JLS) formation. Serial histological sections that were digitalized from 14 embryos at CS20 and CS21 stored at the Kyoto Collection were used for the analysis. Subcutaneous edema and enlargement of the subarachnoid space were found to cause VSC. No obvious abnormalities in cranial regions that may be related to the VSC were detected on histological sections. Three‐dimensional reconstructions revealed the following: (a) the JLS was located bilaterally at the levels between the first and fourth cervical vertebrae; (b) the JLS was pyramidal in shape; and (c) no severe deformity and/or malformation was found in all samples. The JLS was not connected to the subcutaneous tissue and subarachnoid space in all samples. The mean volume of the JLS increased nine‐times from CS20 (0.02 mm3 in VSC [−] group) to CS21 (0.18 mm3 in VSC [−] group). The mean volume of the JLS was comparable between the VSC [−] and VSC (+) groups at both CS20 and CS21. A moderate correlation was observed between VSCd and the mean volume of the JLS in both groups at CS20 (R2 = 0.75) and CS21 (R2 = 0.56). In conclusion, the dynamics of the lymphatic system at the cervical region may contribute to VSC observed around CS21. © 2019 Japanese Teratology Society