Theoretically, ESWL can cause several side effects on the male reproductive system. We determined here the long-term effects of ESWL on sperm with transmission electron microscopy (TEM) in patients with distal ureteral stone. Fifteen men with stones in the distal ureter applied to our clinic formed the group of study. The other 15 men with renal or upper ureter stones formed the group of control. The ESWL sessions, including maximum 19 kW energy level and 3000 shock waves, were performed with Siemens Lithostar ( electromagnetic; Siemens Medical Systems, Erlangen, Germany) lithotriptor. We examined the semen samples from all patients on the day before and 90 days after ESWL. The semen samples were examined with transmission electron microscopy ( TEM) to detect ultrastructural changes on the day before and 90 days after ESWL. All the statistical analyses were realized with SPSS 10.0 ( SPSS Inc., Chicago, USA) statistical package program. When the control and study groups were compared for initial and day 90 sperm concentration and motility, a significant decrease was found in the study group. Although there was no important anomaly in the control group, we determined some damage on sperm structure in 5 patients (33.3%) who are in the study group 3 months after ESWL. It can reduce sperm concentration and motility permanently. It can also cause severe ultrastructural defects on sperm after a long term period in patients with lower ureteral stone. Therefore, we suggest other treatment modalities for young men with distal ureteral stones to prevent the development of male infertility.