This study aimed to evaluate gender differences of hemodialysis patients in adverse events, gastrointestinal bleeding, and bone fractures during 5 year longitudinal follow-up period in the regional core hospital in Japan. This study included 151 patients with maintenance hemodialysis for end-stage renal failure at Takagi Hospital in December 2017. All the patients, divided into females-group of 61 and males-group of 90. Data were evaluated in the electronic medical record. Multivariate analysis indicated a decrease in diabetes mellitus (odd ratio: 2.3, 95% confidence interval: 1.1–4.8,
p
= 0.03) and less mortality in those younger than 75 years old (odd ratio: 0.2, 95% confidence interval: 0.1–0.8,
p
= 0.02) were characterized factors in females. Gastrointestinal bleeding were not different between genders. Bone fractures were high in females (females: 34.4% vs males: 18.9%;
p
<0.03), whereas the mortality rate of bone fractured patients was markedly high in males (females: 28.6% vs males: 76.5%;
p
= 0.003) with lower body bone fractures. In conclusion, diabetes mellitus-induced end-stage renal failure was less common in females. The mortality rate during hemodialysis was higher in males less than 75 years old with increased mortality with lower bone fractures.