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Oral health screening is important for maintaining and improving quality of life. The present study aimed to determine whether patients with a certain level of alveolar bone resorption could be screened by salivary bacterial test along with their background information. Saliva samples were collected from 977 Japanese patients, and the counts of each red-complex, that is, <i>Porphyromonas gingivalis</i>, <i>Treponema denticola</i>, and <i>Tannerella forsythia</i>, were measured using quantitative polymerase chain reaction analysis. Mean bone crest levels (BCLs) were measured using a full-mouth periapical radiograph. Multiple logistic regression analysis was used to determine associations between BCLs (1.5–4.0 mm in 0.5 mm increments) and explanatory variables, such as the number of each red-complex bacteria and the patients’ age, sex, number of teeth, stimulated saliva volume, and smoking habits. When the cutoff BCL value was set at 3.0 mm, the area under the curve, sensitivity, and specificity values were optimal at 0.86, 0.82, and 0.76, respectively. In addition, all tested explanatory variables, except sex and <i>T. denticola</i> count, were significantly associated with BCLs according to a likelihood ratio test (<i>p</i> < 0.05). Additionally, the odds ratio (OR) was substantially increased when a patient was >40 years old and the bacterial count of <i>P. gingivalis</i> was >10⁷ cells/µL (OR: >6). Thus, <i>P. gingivalis</i> count and patients’ background information were significantly associated with the presence of a certain amount of bone resorption, suggesting that it may be possible to screen bone resorption without the need for radiography or oral examination.