Background: One of the methods for evaluating the efficiency of hemodialysis is measurement of serum urea levels before and after dialysis. Because urea is also secreted in the saliva, finding a relation between serum and salivary urea levels can facilitate this evaluation and decrease the frequency of blood sampling. The purpose of this study was to compare changes in the biochemical parameters in serum and saliva in patients before and after hemodialysis. Methods: In this descriptive-analytic study, 43 consenting patients undergoing hemodialysis who met the inclusion criteria were examined. Venous blood was collected before and after hemodialysis. Whole saliva was collected by spitting into sterile tubes for 5 min before and after hemodialysis. The samples were sent to a laboratory for analysis of urea, creatinine, potassium, calcium and phosphorous. The results were compared and analyzed using SPSS17 and p < 0.05 was considered significant. Results: Serum urea, creatinine, potassium and phosphorous levels decreased significantly after hemodialysis in comparison with pre-dialysis levels (p < 0.001). In saliva urea, creatinine and potassium levels decreased significantly after hemodialysis (p < 0.001), but the decrease in calcium and phosphorous were not significant. A significant positive correlation was found between the serum and salivary urea reduction ratio (r = 0.724). Conclusion: It can be concluded that the urea reduction rate in saliva reflected the urea reduction rate of serum, but there was no significant correlation between changes in other parameters in the saliva and serum; however, more studies are needed to develop a practical use of salivary analysis for evaluating hemodialysis patients.