The aim of this study was to evaluate the efficacy of topical subgingival application of doxycycline hyclate (DH) gel adjunctive to non-surgical periodontal therapy on gingival crevicular fluid (GCF) matrix metalloproteinase (MMP)-8 levels in chronic and aggressive periodontitis patients. Forty teeth of 10 chronic periodontitis patients and 32 teeth of eight aggressive periodontitis patients were screened for 6 months. Scaling and root planing (SRP) was applied to the control sites and DH gel adjunctive to SRP was applied to the test sites of each patient simultaneously. GCF MMP-8 levels were analysed at baseline, 7 days; and at 1, 3 and 6 months by Sandwich Elisa Method. At 1, 3 and 6 months, probing depth (P < 0.0051) and plaque scores and bleeding on probing values (P = 0.000) significantly decreased in each group when compared with the baseline, but there was no statistically significant difference between the test and control sites. GCF MMP-8 levels reduced presenting statistically significant differences on 7 days, 1, 3 and 6 months in four of the groups (P < 0.05); however, intergroup differences were not statistically significant. Developing functional and immunological-based chair-side MMP tests might serve as useful adjunctive diagnostic tools when monitoring the effects of DH gel application.