The expression of the phosphoinositides phosphatases Synaptojanins (Synjs) 1 and 2 has been shown in brain and in some peripheral tissues, but their expression in the intestine has not been reported. Herein we show that the small and large intestine express Synj1 and Synj2. Their mRNA levels, measured by RT-PCR, are not affected by development in the small intestine but in the colon they increase with age. Immunostaining assays reveal that both Synjs localize at the apical domain of the epithelial cells and at the lamina propria at sites also expressing the neuron marker calretinin. Synj2 staining at the lamina propria is fainter than that of Synj1. In colonocytes Synjs are at the apical membrane and cytosolic membrane vesicles. Synj2 is also at the mitochondria. Western blots reveal that the intestinal mucosa expresses at least two Synj1 (170- and 139-kDa) and two Synj2 (160- and 148-kDa) isoforms. The observations suggest that Synj1-170, Synj2-160, and Synj2-148 in colonocytes, might participate in processes that take place mainly at the apical domain of the epithelial cells whereas Synj1-139 in those at the enteric nervous system. Experimental colitis augments the mRNA abundance of both Synjs in colon but only Synj2 mRNA levels are increased in colon tumors. In conclusion, as far as we know, this is the first report showing expression, location and isoforms of Synj1 and Synj2 in the small and large intestine and that they might participate in intestinal pathology.