We report here that a truncated 5-HTT protein is produced in the neurons of the raphe, in serotonin transporter (5-HTT) knockout (KO) mice. The 5-HTT gene has exon 2 deleted and we found that one main transcript, shortened by 450 bp, is produced in these KO mice. The mutated 5-HTT protein is only recognized by antibodies against the C-terminal portion of 5-HTT. This protein is not functional as there is no high-affinity serotonin uptake in 5-HTT KO mice, in adults or during development. Conversely, low-affinity serotonin uptake was detected in vitro, and in dopaminergic neurons of the substantia nigra in vivo. The truncated 5-HTT, recognized by antibodies to the C-terminus, is present exclusively in the somatodendritic compartment of the raphe neurons instead of being exported to axons. As shown with confocal and electron microscopy, the truncated 5-HTT does not reach the plasma membrane and is essentially retained in the endoplasmic reticulum. However, this does not seem to trigger refolding or degradation responses, as no upregulation of the chaperone BiP or of the degradation signal ubiquitin was detected. Last, as observed in heterozygous mice, the presence of the truncated 5-HTT protein, although produced in large quantities, does not disturb the normal trafficking of the wild-type protein. This study therefore validates the 5-HTT KO model despite the occurrence of an incomplete translation, and brings novel information on the in vivo 5-HT uptake and cellular processing of an abnormal 5-HTT protein.