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Abstract This study was carried out on 40 male patients suffering from severe refractory acne attending the dermatology outpatient clinic, in Suez Canal University Hospital, Ismailia, Egypt. This study was pre-post interventional study and was done to assess the effect of systemic isotretinoin on semen parameters and sperm ultrastructure by using transmission electron microscopy. Semen analysis was done by computer assisted semen analysis (CASA) according to WHO 2010 criteria before and after the use of systemic isotretinoin, in a relevant private sector (Cleopatra- IVF centerIsmailia) in Ismailia-Egypt. Sperm ultrastructure was evaluated by the transmission electron microscopy, It was done in Al Azhar University, Electron Microscopy Unit also before and after the use of systemic isotretinoin. In the present study the mean age of participants was 33.25 ± 6.75 years (ranged from 21 to 45 years), semen volume showed statistically significant increase after the use of systemic isotretinoin (p<0.001), there was also statistically significant increase in the sperm concentration (p<0.001) from (85.70 million/ml) to (105.0 million/ml) and sperm count per ejaculate (p=0.017) from (171.0 million/ml) to (200.0 million/ml) after the use of systemic isotretinoin. There was statistically significant increase in the progressive motility (p=0.001) from (51%) to (58.50%), there was statistically significant increase in the morphologically normal sperms (p=0.023) from |