Objective To determine the disease prevalence and its relationship with hepatitis B and C viruses among school children in five endemic areas by schistosomiasis. Methods During June 2007 and March 2009, 1 484 school children aged between 5 – 16 years participated in the current study from 32 basic schools in five districts (Al-Dhabab, Hedran, Warazan, Al-Barh and Al-Shmaytin) in Taiz Governorate, Republic of Yemen. Out of school children who participated in the study; 1 406 stool samples, 1 484 urine samples and 214 blood samples were collected and examined. Results Schistosoma mansoni ( S. mansoni) was found in all the studied areas except Al-Barh. However, Schistosoma haematobium ( S. haematobium) was recorded only in Al-Shmaytin and Al-Barh. Both S. mansoni and S. haematobium were observed in Al-Shmaytin district. The overall prevalence was 20.76% for S. mansoni and 7.41% for S. haematobium. The prevalence rate of infection among males was higher than females, shwing no significant differences. Rate of light, moderate and heavy infections in the case of S. mansoni were 41.78%, 25.34% and 32.87% respectively. Whereas, for S. hematobium it was 50.90% for light infection and 49.09% for heavy infection. Regarding to the prevalence of viral hepatitis among infected school children with schistosomiasis, it could be noticed that hepatitis B virus was higher than the prevalence of hepatitis C virus. But, the presence of HBsAg and anti-HCV was not associated with Schistosoma infection. Conclusions Schistosomiasis infection is an important public health problem in Taiz Governorate, Republic of Yemen. There was a correlation between S. haematobium and hepatitis B, but no association between S. mansoni infections and hepatitis B and C viruses.