Stage 13 is short, lasting for about 1 hour (9:20-10:20 h). It is initiated by the completion of germ band shortening, when the prospective anal pads occupy the posterior egg pole and ends with the beginning of head involution.

The clypeolabrum becomes thinner and starts to retract; retraction of the clypeolabrum gives rise ventrally to a conspicuous triangular gap, at the anterior egg pole. At the same time the labium moves to the ventral midline, becoming manifest due to the displacement of the opening of the salivary gland duct. The so-called dorsal fold (dorsal ridge) will appear in the anterior dorsal gap. Posterior and anterior midgut primordia, which have fused in stage 12, form a thin epithelium on either side of the yolk sac.

Cells of the midgut epithelia expand over the yolk sac to make contact along the ventral and dorsal midline and eventually fuse. This process takes quite a long time to be complete, extending into stages 14 and 15.

The hindgut opens in the anus. At the beginning of stage 13 the hindgut consists of an empty longitudinal tube, contiguous with the midgut epithelia. Four thin Malpighian tubules can be distinguished sprouting from its ventral side.

Three different regions can be distinguished in the foregut, the pharynx, consisting of the pharyngeal roof and hypopharyngeal lobes, the prospective esophagus and the proventriculus. The three invaginations of the stomatogastric nervous system have disappeared, their cells becoming distributed within the clypeolabrum.

The two developing salivary gland lobes join to form a common midsagittal duct behind the hypopharyngeal lobes at the beginning of stage 13; the salivary gland duct will be displaced towards the foregut as the labial appendages move frontalward during mouth involution. The salivary glands diverge bilaterally from the common duct, extending between the epidermis and the ventral cord beneath the midgut.

The epidermis of the procephalic lobe and clypeolabrum ends at the interface with the amnioserosa, contiguous with the dorsal ridge. The dorsal ridge during stage 13 extends dorsalwards to fuse eventually across the dorsal midline with ist complement on the other side. After germ band shortening, the dorsal surface of the embryo is formed by the amnioserosa, which is characterized by extremely thin and flat cells that abut the dorsal epidermis. However, during stage 13 the epidermal layer starts to extend dorsally over the amnioserosa towards the dorsal midline, ultimately leading to dorsal closure of the embryo.

The developing central nervous system consists of the well differentiated ventral cord and the supraoesophageal ganglion. Neuromere organization is clearly distinguishable within both the ventral nerve cord and the suboesophageal ganglion. Ventral cord and suboesophageal ganglion extend from the tip of the hypopharyngeal lobe to the region immediately ventral to the anus, and will maintain this length until stage 15, when ventral cord condensation sets in. The primordia of the optic lobes have become integrated into the posteroventral region of the supraoesophageal ganglion, although their cells can still be distinguished cytologically. Fibre connectives and commissures linking the different neuromeres are formed. Progenitors of sensory cells, including the primordia of the antenno-maxillary complex, appear in the epidermis of maxilla, mandible and procephalic lobe. At the end of stage 13 muscle cells become apparent, inserting at incipient apodemes of the lateral epidermis.