Aim: The purpose of this paper is to investigate the prevalence of dental caries and the types of streptococci mutant and Lactobacillus in the saliva of children with middle ear infection (MEI), enlarged tonsils (ET), and healthy children. Materials and methods: A sample of 93 subjects (57 males and 36 females; mean age: 8.1 ± 1 years, aged between 5 years and 15 years old) were assessed: 35 patients, with MEI, and 26 with ET, formed the study group, while 32 healthy subjects formed the control group. The participants were interviewed regarding demographic data, dietary, and oral hygiene habits. Their dental caries and oral hygiene status were clinically determined, assessing diagnostic criteria for decayed, missing, and filled teeth for primary (dmft) and permanent (DMFT) dentition, oral hygiene index according to Greene–Vermillion, and the gingival index (GI) according to Silness–Löe. Stimulated salivary flow rate, and salivary mutans streptococci (MS) and lactobacilli (LB) were also determined. Results: The groups were similar with respect to gender, using fluoride paste, visits to dentist, family income (p > 0.05), whereas there was a difference in age, educational level, method of feeding, use of pacifier, sweet eating habits, toothbrushing, saliva secretion, and rate of oral breathing (p < 0.001) between intervention and healthy group. However, higher salivary MS and LB levels were observed in MEI, and ET patients compared to controls (p < 0.05). Conclusion: Our results demonstrated that patients with ET and MEI had more initial caries, gingival inflammation, dental plaque, a lower stimulated salivary secretion rate, and an increase in the level of salivary MS and LB than healthy individuals. Clinical significance: Results from our study will help not only the pediatric dentistry specialists but also the other medical professionals like pediatricians, ENT specialists, and nurses to increase their awareness regarding the importance of the overall dental health in children with an ear infection or tonsillitis.