Studies suggest that analysis of gingival crevicular fluid (GCF) is useful for evaluating periodontal status. In this study, clinical variables related to tooth mobility, and multiple cytokine levels in proximate GCF, were measured at four time points during initial periodontal treatment: before treatment (baseline), after supragingival scaling, after occlusal adjustment, and after scaling and root planing (SRP); 20 teeth from 13 patients with periodontitis were included. Baseline interleukin (IL)-10 level in GCF was significantly higher around teeth that showed substantial improvement in periodontal epithelial surface area (PESA) after SRP than around teeth without PESA improvement. IL-3 and IL-16 levels in GCF at baseline were significantly higher around teeth with a periodontal inflamed surface area (PISA) of 0 mm2 after SRP than around teeth without PISA improvement. In addition, baseline IL-7, IL-11, and IL-12p40 levels in GCF were significantly lower around teeth with decreased mobility after occlusal adjustment than around teeth without decreased mobility. These results suggest that pre-treatment cytokine levels in GCF are useful in predicting the effects of initial periodontal treatment.