Objective: This study aimed to evaluate oral hygiene status, salivary fluoride concentration, and Streptococcus mutans and Lactobacillus levels in saliva of thalassemic, hemophilic and individuals without any other systemic disorders.Materials and Methods: A total 162 individuals (44 healthy individuals, 86 thalassemic and 32 hemophilic patients) were selected, and randomly (n=30 in each group), the patients were allocated to Group A: individuals without any systemic condition, Group B: thalassemic patients, and Group C: hemophilic patients. Detailed case history, DMFT/DMFS, and OHI-S index were recorded. An aliquot of 5 ml of saliva was collected from each patient to determine the salivary fluoride concentration and predominant microbial colony in saliva. The data were analyzed by chi-square test of independence and nonparametric Kruskal-Wallis H test.Results: The mean debris and calculus index among groups A, B, and C was 0.55 ± 0.43, 0.61 ± 0.46, 0.46 ± 0.47 and 0.33 ± 0.48, 0.18 ± 0.34, and 0.15 ± 0.34, respectively. The DMFT score for group A was high (1.93 ± 1.86, 1.67 ± 1.92) compared to groups B (0.40 ± 0.77, 0.67 ± 1.37) and C (0.47 ± 0.68, 0.30 ± 0.54). The fluoride concentrations among three groups (A, B, and C) were 0.06 ± 0.07, 0.12 ± 0.13, and 0.12 ± 0.13 ppm respectively. The number of colony-forming units was highest in the healthy individual>hemophilic>thalassemic and presence of predominant microorganisms showed insignificant association among the groups (p=0.323).Conclusion: Compared to healthy individuals, thalassemic and hemophilic patients had better oral hygiene.