The present study aimed to compare the efficacy of conventional initial periodontal treatment (C-IPT), full-mouth disinfection IPT (FMD-IPT) and full-mouth IPT (FM-IPT) and the levels of gingival crevicular fluid interleukin-1β (IL-1β) and interleukin-17 (IL-17), Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Fusobacterium nucleatum, Prevotella intermedia, Parvimonas micra and Campylobacter rectus in patients with generalized aggressive periodontitis (GAgP) over 6-months period. Forty-two GAgP patients were randomly assigned into 3 groups. IPT was performed in a quadrant-wise manner at 1-week intervals in C-IPT, in 2 sessions within 24 hours in FM-IPT, and in 2 sessions with application of chlorhexidine to the intra-oral niches within 24 hours in FMD-IPT. FMD-IPT group also used daily 0,2% chlorhexidine for 3 weeks. At baseline, 3 and 6 months clinical parameters consisting of plaque index, gingival index, probing depth, bleeding on probing and clinical attachment level were recorded, gingival crevicular fluid and microbiological samples were collected. Gingival crevicular fluid levels of IL-1β and IL-17 were analyzed using ELISA. The quantitative real-time polymerase chain reaction method was used for the quantitative detection of periodontal pathogens.