AIM: To investigate the variation of IGSF3 gene in three families with congenital absence of lacrimal puncta and canaliculi, and to lay a foundation for further research on the pathogenic gene of congenital lacrimal duct agenesis. METHODS: The members of the three families were recruited. The ophthalmologic examinations in details, including slit-lamp biomicroscope, intraocular pressure and fundus examination, etc. were carried out. All patients were checked with paracentesis of puncta membrane and lacrimal duct probing, as well as the computed tomography-dacryocystography (CT-DCG). Peripheral blood of 14 participants (3 normal) from three families were collected, 4 mL each, for genomic DNA extraction, and 11 exon fragments of IGSF3 gene were amplified and sequenced by polymerase chain reaction (PCR) to determine whether there were IGSF3 genetic variation. RESULTS: A total of 14 members from three families were screened for 4 synonymous variants: c.930C>T (p.Pro366=), c.1359T>C (p.Ser709=), c.1797G>A (p.Ser855=), c.1539G>A (p.Ser769=), and 6 missense variants: c.1507G>A (p.Gly759Ser), c.1783T>C (p.Trp851Arg), c.1952G>T (p.Ser 907Ile), c.3120C>G (p.Asp1040Glu), c.3123C>G (p.Asp1041Glu), c.3139_3140insGAC (p.Asp1046_Pro1047insAsp), and the latter three were only found in two patients with absence of lacrimal puncta and canaliculi combined with congenital osseous nasolacrimal canal obstruction from the first family. CONCLUSION: The same IGSF3 gene mutation c.3139_3140insGAC is found in the patients with congenital absence of lacrimal puncta and canaliculi combine with osseous nasolacrimal canal obstruction.