The aim was to compare the peri-implant clinical and radiographic inflammatory parameters and whole salivary cotinine levels among cigarette smokers (CS), waterpipe smokers (WS) and never-smokers (NS). Thirty-four CS (Group 1), 33 WS (Group 2), and 31 NS (Group 3) were included. Peri-implant plaque index (PI), bleeding-on-probing (BOP), and probing depth (PD) were measured, and crestal bone loss (CBL) was assessed on standardized digital radiographs. Unstimulated whole saliva samples were collected and whole salivary cotinine levels were measured. Peri-implant PI and PD were higher in Groups 1 (P < 0.05) and 2 (P < 0.05) than in Group 3. Peri-implant BOP was significantly higher in Group 3 than in Groups 1 (P < 0.01) and 2 (P < 0.01). Peri-implant MBL was significantly higher in Groups 1 (P < 0.05) and 2 (P < 0.05) than in Group 3. There were significant differences in PI, BOP, PD, and CBL between Groups 1 and 2. There was no significant difference in the whole salivary cotinine levels in Groups 1 and 2. Peri-implant sites with plaque accumulation, PD, CBL, and whole salivary cotinine levels were higher in CS and WS than in NS, but did not differ between CS and WS.