Background and Aim: Chemotherapeutic agents are adjunctive substances for treatment of periodontitis through modulation of host response. Sodium alendronate is one of the medicaments which are used for this purpose. Since alkaline phosphates (ALP) level is an indicator for evaluation of bone metabolism changes, in this study the effect of sodium alendronate on periodontitis is investigated by measuring gingival crevicular fluid alkaline phosphates (GCF ALP) levels.Materials and Methods: In this double-blind experimental study, 24 patients (12 males and 12 females between the agen of 35 to 50 years) with moderate chronic periodontitis have been evaluated. All patients received scaling and root planning. Sodium alendronate and placebo capsules were used weekly in a period of six months for case and control groups respectively samples were collected in first visit, 3 months, and 6 month later and analyzed with spectrophotometry. Periodontal assessments were probing pocket depth, gingival index (loe and silness) and plaque index (silness and loe). Data were analyzed by t-test, repeated measurement paired t-test.Results: Mean changes of GCF ALP optical absorbtion were significant in case group through the period of 6 months, and in control group through the period of 3 months, however after 6 months in control group there is no significant changes in comparison with base line evaluations. During the study GCF ALP changes between two group were not significant statically. Mean changes of plaque index and gingival index were statically significant in both groups through 6 months period. Plaque index variations were significantly different between two groups. But duration of gingival index changes between 2 groups was insignificant.Conclusion: The use of sodium alendronate for 6 months improves periodontal parameters and decrease GCF ALP level, but these results are not so significant during this period of time.